From 1ed8d02e2c68a31ae0b5bd0b08e0f0c7f9d1a64e Mon Sep 17 00:00:00 2001 From: Berk Hess Date: Wed, 28 Jul 2010 10:54:40 +0200 Subject: [PATCH] amber ff atomtypes change: corrected masses, removed bonded atom types, added atomic numbers, changed comments to the original Amber file comments --- share/top/amber03.ff/atomtypes.atp | 136 ++++++++++++------------ share/top/amber03.ff/ffnonbonded.itp | 155 ++++++++++++++-------------- share/top/amber94.ff/atomtypes.atp | 134 ++++++++++++------------ share/top/amber94.ff/ffnonbonded.itp | 153 ++++++++++++++------------- share/top/amber96.ff/atomtypes.atp | 134 ++++++++++++------------ share/top/amber96.ff/ffnonbonded.itp | 153 ++++++++++++++------------- share/top/amber99.ff/atomtypes.atp | 134 ++++++++++++------------ share/top/amber99.ff/ffnonbonded.itp | 153 ++++++++++++++------------- share/top/amber99sb-ildn.ff/atomtypes.atp | 134 ++++++++++++------------ share/top/amber99sb-ildn.ff/ffnonbonded.itp | 153 ++++++++++++++------------- share/top/amber99sb.ff/atomtypes.atp | 134 ++++++++++++------------ share/top/amber99sb.ff/ffnonbonded.itp | 153 ++++++++++++++------------- share/top/amberGS.ff/atomtypes.atp | 134 ++++++++++++------------ share/top/amberGS.ff/ffnonbonded.itp | 153 ++++++++++++++------------- 14 files changed, 989 insertions(+), 1024 deletions(-) rewrite share/top/amber03.ff/atomtypes.atp (87%) rewrite share/top/amber03.ff/ffnonbonded.itp (93%) rewrite share/top/amber94.ff/atomtypes.atp (87%) rewrite share/top/amber94.ff/ffnonbonded.itp (93%) rewrite share/top/amber96.ff/atomtypes.atp (87%) rewrite share/top/amber96.ff/ffnonbonded.itp (93%) rewrite share/top/amber99.ff/atomtypes.atp (87%) rewrite share/top/amber99.ff/ffnonbonded.itp (93%) rewrite share/top/amber99sb-ildn.ff/atomtypes.atp (87%) rewrite share/top/amber99sb-ildn.ff/ffnonbonded.itp (93%) rewrite share/top/amber99sb.ff/atomtypes.atp (87%) rewrite share/top/amber99sb.ff/ffnonbonded.itp (93%) rewrite share/top/amberGS.ff/atomtypes.atp (87%) rewrite share/top/amberGS.ff/ffnonbonded.itp (93%) diff --git a/share/top/amber03.ff/atomtypes.atp b/share/top/amber03.ff/atomtypes.atp dissimilarity index 87% index 3968548d33..1c7e44cf60 100644 --- a/share/top/amber03.ff/atomtypes.atp +++ b/share/top/amber03.ff/atomtypes.atp @@ -1,69 +1,67 @@ -H0 1.00800 ; H0 H aliph. bond. to C with 1 electrwd. group (03GLY) -Br 79.90000 ; BR bromine -C 12.01000 ; C sp2 C carbonyl group -CA 12.01000 ; CA sp2 C pure aromatic (benzene) -CB 12.01000 ; CB sp2 aromatic C, 5&6 membered ring junction -CC 12.01000 ; CC sp2 aromatic C, 5 memb. ring HIS -CK 12.01000 ; CK sp2 C 5 memb.ring in purines -CM 12.01000 ; CM sp2 C pyrimidines in pos. 5 & 6 -CN 12.01000 ; CN sp2 C aromatic 5&6 memb.ring junct.(TRP) -CQ 12.01000 ; CQ sp2 C in 5 mem.ring of purines between 2 N -CR 12.01000 ; CR sp2 arom as CQ but in HIS -CT 12.01000 ; CT sp3 aliphatic C -CV 12.01000 ; CV sp2 arom. 5 memb.ring w/1 N and 1 H (HIS) -CW 12.01000 ; CW sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS) -C* 12.01000 ; C* sp2 arom. 5 memb.ring w/1 subst. (TRP) -C0 40.08000 ; Ca2+ calcium -F 19.00000 ; F fluorine -H 1.00800 ; H H bonded to nitrogen atoms -HC 1.00800 ; HC H aliph. bond. to C without electrwd.group -H1 1.00800 ; H1 H aliph. bond. to C with 1 electrwd. group -H2 1.00800 ; H2 H aliph. bond. to C with 2 electrwd.groups -H3 1.00800 ; H3 H aliph. bond. to C with 3 eletrwd.groups -HA 1.00800 ; HA H arom. bond. to C without elctrwd. groups -H4 1.00800 ; H4 H arom. bond. to C with 1 electrwd. group -H5 1.00800 ; H5 H arom. bond. to C with 2 electrwd. groups -HO 1.00800 ; HO hydroxyl group -HS 1.00800 ; HS hydrogen bonded to sulphur -HW 1.00800 ; HW H in TIP3P water -HP 1.00800 ; HP H bonded to C next to positively charged gr -I 126.90000 ; I iodine -Cl 35.45000 ; Cl- -Na 22.99000 ; Na+ -IB 131.00000 ; IB 'big ion w/ waters' for vacuum (Na+, 6H2O) -MG 24.30000 ; Mg2+ magnesium -N 14.01000 ; N sp2 nitrogen in amide groups -NA 14.01000 ; NA sp2 N in 5 memb.ring w/H atom (HIS) -NB 14.01000 ; NB sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) -NC 14.01000 ; NC sp2 N in 6 memb.ring w/LP (ADE,GUA) -N2 14.01000 ; N2 sp2 N in amino groups -N3 14.01000 ; N3 sp3 N for charged amino groups (Lys, etc) -N* 14.01000 ; N* sp2 N -O 16.00000 ; O carbonyl group oxygen -OW 16.00000 ; OW oxygen in TIP3P water -OH 16.00000 ; OH oxygen in hydroxyl group -OS 16.00000 ; OS ether and ester oxygen -O2 16.00000 ; O2 carboxyl and phosphate group oxygen -P 30.97000 ; P phosphate -S 32.06000 ; S sulphur in disulfide linkage -SH 32.06000 ; SH sulphur in cystine -CU 63.55000 ; CU copper -FE 55.00000 ; FE iron -K 39.10000 ; K+ potassium -Rb 85.47000 ; Rb+ rubidium -Cs 132.90000 ; Cs+ cesium -OW_spc 15.99940 ; SPC Water OW -HW_spc 1.00800 ; SPC Water HW -Li 6.94000 ; Li+ from parm94/96 -Zn 65.40000 ; Zn2+ from parm99 -HW_tip4pew 1.00800 ; tip4pEW HW -OW_tip4pew 16.00000 ; tip4pEW OW -HW_tip4p 1.00800 ; tip4p HW -OW_tip4p 16.00000 ; tip4p OW -HW_tip5p 1.00800 ; tip5p HW -OW_tip5p 16.00000 ; tip5p OW -HW_tip3p 4.03200 ; TIP3P HEAVY dummy water HW -OW_tip3p 9.95200 ; TIP3P heavy dummy water OW -MW 0.00000 ; Dummy mass for tip4p/5p water extra point charge -MCH3 0.00000 ; Dummy mass in rigid tetrahedral CH3 group -MNH3 0.00000 ; Dummy mass in rigid tetrahedral NH3 group +H0 1.00800 ; H aliph. bond. to C with 1 electrwd. group (03GLY) +Br 79.90000 ; bromine +C 12.01000 ; sp2 C carbonyl group +CA 12.01000 ; sp2 C pure aromatic (benzene) +CB 12.01000 ; sp2 aromatic C, 5&6 membered ring junction +CC 12.01000 ; sp2 aromatic C, 5 memb. ring HIS +CK 12.01000 ; sp2 C 5 memb.ring in purines +CM 12.01000 ; sp2 C pyrimidines in pos. 5 & 6 +CN 12.01000 ; sp2 C aromatic 5&6 memb.ring junct.(TRP) +CQ 12.01000 ; sp2 C in 5 mem.ring of purines between 2 N +CR 12.01000 ; sp2 arom as CQ but in HIS +CT 12.01000 ; sp3 aliphatic C +CV 12.01000 ; sp2 arom. 5 memb.ring w/1 N and 1 H (HIS) +CW 12.01000 ; sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS) +C* 12.01000 ; sp2 arom. 5 memb.ring w/1 subst. (TRP) +C0 40.08000 ; calcium +F 19.00000 ; fluorine +H 1.00800 ; H bonded to nitrogen atoms +HC 1.00800 ; H aliph. bond. to C without electrwd.group +H1 1.00800 ; H aliph. bond. to C with 1 electrwd. group +H2 1.00800 ; H aliph. bond. to C with 2 electrwd.groups +H3 1.00800 ; H aliph. bond. to C with 3 eletrwd.groups +HA 1.00800 ; H arom. bond. to C without elctrwd. groups +H4 1.00800 ; H arom. bond. to C with 1 electrwd. group +H5 1.00800 ; H arom. bond. to C with 2 electrwd. groups +HO 1.00800 ; hydroxyl group +HS 1.00800 ; hydrogen bonded to sulphur (pol?) +HW 1.00800 ; H in TIP3P water +HP 1.00800 ; H bonded to C next to positively charged gr +I 126.90000 ; iodine (Applequist) +Cl 35.45000 ; chlorine (Applequist) +Na 22.99000 ; Na+, ions pol:J.PhysC,11,1541,(1978) +IB 131.00000 ; 'big ion w/ waters' for vacuum (Na+, 6H2O) +MG 24.30500 ; magnesium +N 14.01000 ; sp2 nitrogen in amide groups +NA 14.01000 ; sp2 N in 5 memb.ring w/H atom (HIS) +NB 14.01000 ; sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) +NC 14.01000 ; sp2 N in 6 memb.ring w/LP (ADE,GUA) +N2 14.01000 ; sp2 N in amino groups +N3 14.01000 ; sp3 N for charged amino groups (Lys, etc) +N* 14.01000 ; sp2 N +O 16.00000 ; carbonyl group oxygen +OW 16.00000 ; oxygen in TIP3P water +OH 16.00000 ; oxygen in hydroxyl group +OS 16.00000 ; ether and ester oxygen +O2 16.00000 ; carboxyl and phosphate group oxygen +P 30.97000 ; phosphate,pol:JACS,112,8543,90,K.J.Miller +S 32.06000 ; S in disulfide linkage,pol:JPC,102,2399,98 +SH 32.06000 ; S in cystine +CU 63.55000 ; copper +FE 55.00000 ; iron +K 39.10000 ; potassium +Rb 85.47000 ; rubidium +Cs 132.90000 ; cesium +OW_spc 15.99940 ; SPC Water OW +HW_spc 1.00800 ; SPC Water HW +Li 6.94000 ; lithium, ions pol:J.PhysC,11,1541,(1978) +Zn 65.40000 ; Zn2+ +HW_tip4pew 1.00800 ; tip4pEW HW +OW_tip4pew 16.00000 ; tip4pEW OW +HW_tip4p 1.00800 ; tip4p HW +OW_tip4p 16.00000 ; tip4p OW +HW_tip5p 1.00800 ; tip5p HW +OW_tip5p 16.00000 ; tip5p OW +MW 0.00000 ; Virtual site for tip4p/5p water point charge +MCH3 0.00000 ; Dummy mass in rigid tetrahedral CH3 group +MNH3 0.00000 ; Dummy mass in rigid tetrahedral NH3 group diff --git a/share/top/amber03.ff/ffnonbonded.itp b/share/top/amber03.ff/ffnonbonded.itp dissimilarity index 93% index 4c0efc240e..24e54031e0 100644 --- a/share/top/amber03.ff/ffnonbonded.itp +++ b/share/top/amber03.ff/ffnonbonded.itp @@ -1,79 +1,76 @@ -[ atomtypes ] -; name bond_type mass charge ptype sigma epsilon -H0 H0 0.0000 0.0000 A 2.47135e-01 6.56888e-02 -Br BR 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -C C 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CA CA 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CB CB 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CC CC 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CK CK 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CM CM 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CN CN 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CQ CQ 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CR CR 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CT CT 0.0000 0.0000 A 3.39967e-01 4.57730e-01 -CV CV 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CW CW 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -C* C* 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -C0 Ca 0.0000 0.0000 A 3.05240e-01 1.92376e+00 -F F 0.0000 0.0000 A 3.11815e-01 2.55224e-01 -H H 0.0000 0.0000 A 1.06908e-01 6.56888e-02 -HC HC 0.0000 0.0000 A 2.64953e-01 6.56888e-02 -H1 H1 0.0000 0.0000 A 2.47135e-01 6.56888e-02 -H2 H2 0.0000 0.0000 A 2.29317e-01 6.56888e-02 -H3 H3 0.0000 0.0000 A 2.11499e-01 6.56888e-02 -HA HA 0.0000 0.0000 A 2.59964e-01 6.27600e-02 -H4 H4 0.0000 0.0000 A 2.51055e-01 6.27600e-02 -H5 H5 0.0000 0.0000 A 2.42146e-01 6.27600e-02 -HO HO 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -HS HS 0.0000 0.0000 A 1.06908e-01 6.56888e-02 -HW HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -HP HP 0.0000 0.0000 A 1.95998e-01 6.56888e-02 -I I 0.0000 0.0000 A 4.18722e-01 1.67360e+00 -Cl Cl 0.0000 0.0000 A 4.40104e-01 4.18400e-01 -Na Na 0.0000 0.0000 A 3.32840e-01 1.15897e-02 -IB IB 0.0000 0.0000 A 8.90899e-01 4.18400e-01 -MG Mg 0.0000 0.0000 A 1.41225e-01 3.74342e+00 -N N 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -NA NA 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -NB NB 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -NC NC 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -N2 N2 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -N3 N3 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -N* N* 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -O O 0.0000 0.0000 A 2.95992e-01 8.78640e-01 -OW OW 0.0000 0.0000 A 3.15061e-01 6.36386e-01 -OH OH 0.0000 0.0000 A 3.06647e-01 8.80314e-01 -OS OS 0.0000 0.0000 A 3.00001e-01 7.11280e-01 -O2 O2 0.0000 0.0000 A 2.95992e-01 8.78640e-01 -P P 0.0000 0.0000 A 3.74177e-01 8.36800e-01 -S S 0.0000 0.0000 A 3.56359e-01 1.04600e+00 -SH SH 0.0000 0.0000 A 3.56359e-01 1.04600e+00 -CU CU 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -FE FE 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -K K 0.0000 0.0000 A 4.73602e-01 1.37235e-03 -Rb Rb 0.0000 0.0000 A 5.26699e-01 7.11280e-04 -Cs Cs 0.0000 0.0000 A 6.04920e-01 3.37230e-04 -; spc water - use only with spc.itp & settles -OW_spc OW 0.0000 0.0000 A 3.16557e-01 6.50629e-01 -HW_spc HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -Li Li 0.0000 0.0000 A 2.02590e-01 7.65672e-02 -Zn Zn 0.0000 0.0000 A 1.95998e-01 5.23000e-02 -;tip4p-EW -HW_tip4pew HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -OW_tip4pew OW 0.0000 0.0000 A 3.16435e-01 6.80946e-01 -; tip4p -HW_tip4p HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -OW_tip4p OW 0.0000 0.0000 A 3.15365e-01 6.48520e-01 -;tip5p -HW_tip5p HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -OW_tip5p OW 0.0000 0.0000 A 3.12000e-01 6.69440e-01 -;tip3p heavy -HW_tip3p HW 4.0320 0.0000 A 0.00000e+00 0.00000e+00 -OW_tip3p OW 9.9520 0.0000 A 3.15061e-01 6.36386e-01 -; dummy defs -; MW=Dummy mass for tip4p/EW/5p water extra point charge -MW MW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -; Dummy masses for rigid CH3 and NH3 groups -MCH3 MCH3 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -MNH3 MNH3 0.0000 0.0000 A 0.00000e+00 0.00000e+00 +[ atomtypes ] +; name at.num mass charge ptype sigma epsilon +H0 1 1.008 0.0000 A 2.47135e-01 6.56888e-02 +Br 35 79.90 0.0000 A 0.00000e+00 0.00000e+00 +C 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CA 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CB 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CC 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CK 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CM 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CN 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CQ 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CR 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CT 6 12.01 0.0000 A 3.39967e-01 4.57730e-01 +CV 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CW 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +C* 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +C0 20 40.08 0.0000 A 3.05240e-01 1.92376e+00 +F 9 19.00 0.0000 A 3.11815e-01 2.55224e-01 +H 1 1.008 0.0000 A 1.06908e-01 6.56888e-02 +HC 1 1.008 0.0000 A 2.64953e-01 6.56888e-02 +H1 1 1.008 0.0000 A 2.47135e-01 6.56888e-02 +H2 1 1.008 0.0000 A 2.29317e-01 6.56888e-02 +H3 1 1.008 0.0000 A 2.11499e-01 6.56888e-02 +HA 1 1.008 0.0000 A 2.59964e-01 6.27600e-02 +H4 1 1.008 0.0000 A 2.51055e-01 6.27600e-02 +H5 1 1.008 0.0000 A 2.42146e-01 6.27600e-02 +HO 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +HS 1 1.008 0.0000 A 1.06908e-01 6.56888e-02 +HW 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +HP 1 1.008 0.0000 A 1.95998e-01 6.56888e-02 +I 53 126.9 0.0000 A 4.18722e-01 1.67360e+00 +Cl 17 35.45 0.0000 A 4.40104e-01 4.18400e-01 +Na 11 22.99 0.0000 A 3.32840e-01 1.15897e-02 +IB 0 131.0 0.0000 A 8.90899e-01 4.18400e-01 +MG 12 24.305 0.0000 A 1.41225e-01 3.74342e+00 +N 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +NA 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +NB 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +NC 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +N2 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +N3 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +N* 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +O 8 16.00 0.0000 A 2.95992e-01 8.78640e-01 +OW 8 16.00 0.0000 A 3.15061e-01 6.36386e-01 +OH 8 16.00 0.0000 A 3.06647e-01 8.80314e-01 +OS 8 16.00 0.0000 A 3.00001e-01 7.11280e-01 +O2 8 16.00 0.0000 A 2.95992e-01 8.78640e-01 +P 15 30.97 0.0000 A 3.74177e-01 8.36800e-01 +S 16 32.06 0.0000 A 3.56359e-01 1.04600e+00 +SH 16 32.06 0.0000 A 3.56359e-01 1.04600e+00 +CU 29 63.55 0.0000 A 3.39967e-01 3.59824e-01 +FE 26 55.00 0.0000 A 0.00000e+00 0.00000e+00 +K 19 39.10 0.0000 A 4.73602e-01 1.37235e-03 +Rb 37 85.47 0.0000 A 5.26699e-01 7.11280e-04 +Cs 55 132.91 0.0000 A 6.04920e-01 3.37230e-04 +; spc water - use only with spc.itp & settles +OW_spc 8 15.9994 0.0000 A 3.16557e-01 6.50629e-01 +HW_spc 1 1.0080 0.0000 A 0.00000e+00 0.00000e+00 +Li 3 6.94 0.0000 A 2.02590e-01 7.65672e-02 +Zn 30 65.4 0.0000 A 1.95998e-01 5.23000e-02 +;tip4p-EW +HW_tip4pew 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +OW_tip4pew 8 16.00 0.0000 A 3.16435e-01 6.80946e-01 +; tip4p +HW_tip4p 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +OW_tip4p 8 16.00 0.0000 A 3.15365e-01 6.48520e-01 +;tip5p +HW_tip5p 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +OW_tip5p 8 16.00 0.0000 A 3.12000e-01 6.69440e-01 +; dummy defs +; MW=Dummy mass for tip4p/EW/5p water extra point charge +MW 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 +; Dummy masses for rigid CH3 and NH3 groups +MCH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 +MNH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 diff --git a/share/top/amber94.ff/atomtypes.atp b/share/top/amber94.ff/atomtypes.atp dissimilarity index 87% index 1edd14f6ae..a31392919a 100644 --- a/share/top/amber94.ff/atomtypes.atp +++ b/share/top/amber94.ff/atomtypes.atp @@ -1,68 +1,66 @@ -Br 79.90000 ; BR bromine -C 12.01000 ; C sp2 C carbonyl group -CA 12.01000 ; CA sp2 C pure aromatic (benzene) -CB 12.01000 ; CB sp2 aromatic C, 5&6 membered ring junction -CC 12.01000 ; CC sp2 aromatic C, 5 memb. ring HIS -CK 12.01000 ; CK sp2 C 5 memb.ring in purines -CM 12.01000 ; CM sp2 C pyrimidines in pos. 5 & 6 -CN 12.01000 ; CN sp2 C aromatic 5&6 memb.ring junct.(TRP) -CQ 12.01000 ; CQ sp2 C in 5 mem.ring of purines between 2 N -CR 12.01000 ; CR sp2 arom as CQ but in HIS -CT 12.01000 ; CT sp3 aliphatic C -CV 12.01000 ; CV sp2 arom. 5 memb.ring w/1 N and 1 H (HIS) -CW 12.01000 ; CW sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS) -C* 12.01000 ; C* sp2 arom. 5 memb.ring w/1 subst. (TRP) -C0 40.08000 ; Ca2+ calcium -F 19.00000 ; F fluorine -H 1.00800 ; H H bonded to nitrogen atoms -HC 1.00800 ; HC H aliph. bond. to C without electrwd.group -H1 1.00800 ; H1 H aliph. bond. to C with 1 electrwd. group -H2 1.00800 ; H2 H aliph. bond. to C with 2 electrwd.groups -H3 1.00800 ; H3 H aliph. bond. to C with 3 eletrwd.groups -HA 1.00800 ; HA H arom. bond. to C without elctrwd. groups -H4 1.00800 ; H4 H arom. bond. to C with 1 electrwd. group -H5 1.00800 ; H5 H arom. bond. to C with 2 electrwd. groups -HO 1.00800 ; HO hydroxyl group -HS 1.00800 ; HS hydrogen bonded to sulphur -HW 1.00800 ; HW H in TIP3P water -HP 1.00800 ; HP H bonded to C next to positively charged gr -I 126.90000 ; I iodine -Cl 35.45000 ; Cl- -Na 22.99000 ; Na+ -IB 131.00000 ; IB 'big ion w/ waters' for vacuum (Na+, 6H2O) -MG 24.30000 ; Mg2+ magnesium -N 14.01000 ; N sp2 nitrogen in amide groups -NA 14.01000 ; NA sp2 N in 5 memb.ring w/H atom (HIS) -NB 14.01000 ; NB sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) -NC 14.01000 ; NC sp2 N in 6 memb.ring w/LP (ADE,GUA) -N2 14.01000 ; N2 sp2 N in amino groups -N3 14.01000 ; N3 sp3 N for charged amino groups (Lys, etc) -N* 14.01000 ; N* sp2 N -O 16.00000 ; O carbonyl group oxygen -OW 16.00000 ; OW oxygen in TIP3P water -OH 16.00000 ; OH oxygen in hydroxyl group -OS 16.00000 ; OS ether and ester oxygen -O2 16.00000 ; O2 carboxyl and phosphate group oxygen -P 30.97000 ; P phosphate -S 32.06000 ; S sulphur in disulfide linkage -SH 32.06000 ; SH sulphur in cystine -CU 63.55000 ; CU copper -FE 55.00000 ; FE iron -K 39.10000 ; K+ potassium -Rb 85.47000 ; Rb+ rubidium -Cs 132.90000 ; Cs+ cesium -OW_spc 15.99940 ; SPC Water OW -HW_spc 1.00800 ; SPC Water HW -Li 6.94000 ; Li+ from parm94/96 -Zn 65.40000 ; Zn2+ from parm99 -HW_tip4pew 1.00800 ; tip4pEW HW -OW_tip4pew 16.00000 ; tip4pEW OW -HW_tip4p 1.00800 ; tip4p HW -OW_tip4p 16.00000 ; tip4p OW -HW_tip5p 1.00800 ; tip5p HW -OW_tip5p 16.00000 ; tip5p OW -HW_tip3p 4.03200 ; TIP3P HEAVY dummy water HW -OW_tip3p 9.95200 ; TIP3P heavy dummy water OW -MW 0.00000 ; Dummy mass for tip4p/5p water extra point charge -MCH3 0.00000 ; Dummy mass in rigid tetrahedral CH3 group -MNH3 0.00000 ; Dummy mass in rigid tetrahedral NH3 group +Br 79.90000 ; bromine +C 12.01000 ; sp2 C carbonyl group +CA 12.01000 ; sp2 C pure aromatic (benzene) +CB 12.01000 ; sp2 aromatic C, 5&6 membered ring junction +CC 12.01000 ; sp2 aromatic C, 5 memb. ring HIS +CK 12.01000 ; sp2 C 5 memb.ring in purines +CM 12.01000 ; sp2 C pyrimidines in pos. 5 & 6 +CN 12.01000 ; sp2 C aromatic 5&6 memb.ring junct.(TRP) +CQ 12.01000 ; sp2 C in 5 mem.ring of purines between 2 N +CR 12.01000 ; sp2 arom as CQ but in HIS +CT 12.01000 ; sp3 aliphatic C +CV 12.01000 ; sp2 arom. 5 memb.ring w/1 N and 1 H (HIS) +CW 12.01000 ; sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS) +C* 12.01000 ; sp2 arom. 5 memb.ring w/1 subst. (TRP) +C0 40.08000 ; calcium +F 19.00000 ; fluorine +H 1.00800 ; H bonded to nitrogen atoms +HC 1.00800 ; H aliph. bond. to C without electrwd.group +H1 1.00800 ; H aliph. bond. to C with 1 electrwd. group +H2 1.00800 ; H aliph. bond. to C with 2 electrwd.groups +H3 1.00800 ; H aliph. bond. to C with 3 eletrwd.groups +HA 1.00800 ; H arom. bond. to C without elctrwd. groups +H4 1.00800 ; H arom. bond. to C with 1 electrwd. group +H5 1.00800 ; H arom. bond. to C with 2 electrwd. groups +HO 1.00800 ; hydroxyl group +HS 1.00800 ; hydrogen bonded to sulphur (pol?) +HW 1.00800 ; H in TIP3P water +HP 1.00800 ; H bonded to C next to positively charged gr +I 126.90000 ; iodine (Applequist) +Cl 35.45000 ; chlorine (Applequist) +Na 22.99000 ; Na+, ions pol:J.PhysC,11,1541,(1978) +IB 131.00000 ; 'big ion w/ waters' for vacuum (Na+, 6H2O) +MG 24.30500 ; magnesium +N 14.01000 ; sp2 nitrogen in amide groups +NA 14.01000 ; sp2 N in 5 memb.ring w/H atom (HIS) +NB 14.01000 ; sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) +NC 14.01000 ; sp2 N in 6 memb.ring w/LP (ADE,GUA) +N2 14.01000 ; sp2 N in amino groups +N3 14.01000 ; sp3 N for charged amino groups (Lys, etc) +N* 14.01000 ; sp2 N +O 16.00000 ; carbonyl group oxygen +OW 16.00000 ; oxygen in TIP3P water +OH 16.00000 ; oxygen in hydroxyl group +OS 16.00000 ; ether and ester oxygen +O2 16.00000 ; carboxyl and phosphate group oxygen +P 30.97000 ; phosphate,pol:JACS,112,8543,90,K.J.Miller +S 32.06000 ; S in disulfide linkage,pol:JPC,102,2399,98 +SH 32.06000 ; S in cystine +CU 63.55000 ; copper +FE 55.00000 ; iron +K 39.10000 ; potassium +Rb 85.47000 ; rubidium +Cs 132.90000 ; cesium +OW_spc 15.99940 ; SPC Water OW +HW_spc 1.00800 ; SPC Water HW +Li 6.94000 ; lithium, ions pol:J.PhysC,11,1541,(1978) +Zn 65.40000 ; Zn2+ +HW_tip4pew 1.00800 ; tip4pEW HW +OW_tip4pew 16.00000 ; tip4pEW OW +HW_tip4p 1.00800 ; tip4p HW +OW_tip4p 16.00000 ; tip4p OW +HW_tip5p 1.00800 ; tip5p HW +OW_tip5p 16.00000 ; tip5p OW +MW 0.00000 ; Virtual site for tip4p/5p water point charge +MCH3 0.00000 ; Dummy mass in rigid tetrahedral CH3 group +MNH3 0.00000 ; Dummy mass in rigid tetrahedral NH3 group diff --git a/share/top/amber94.ff/ffnonbonded.itp b/share/top/amber94.ff/ffnonbonded.itp dissimilarity index 93% index 7dd6009240..ef3fde6d98 100644 --- a/share/top/amber94.ff/ffnonbonded.itp +++ b/share/top/amber94.ff/ffnonbonded.itp @@ -1,78 +1,75 @@ -[ atomtypes ] -; name bond_type mass charge ptype sigma epsilon -Br BR 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -C C 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CA CA 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CB CB 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CC CC 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CK CK 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CM CM 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CN CN 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CQ CQ 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CR CR 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CT CT 0.0000 0.0000 A 3.39967e-01 4.57730e-01 -CV CV 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CW CW 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -C* C* 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -C0 Ca 0.0000 0.0000 A 3.05240e-01 1.92376e+00 -F F 0.0000 0.0000 A 3.11815e-01 2.55224e-01 -H H 0.0000 0.0000 A 1.06908e-01 6.56888e-02 -HC HC 0.0000 0.0000 A 2.64953e-01 6.56888e-02 -H1 H1 0.0000 0.0000 A 2.47135e-01 6.56888e-02 -H2 H2 0.0000 0.0000 A 2.29317e-01 6.56888e-02 -H3 H3 0.0000 0.0000 A 2.11499e-01 6.56888e-02 -HA HA 0.0000 0.0000 A 2.59964e-01 6.27600e-02 -H4 H4 0.0000 0.0000 A 2.51055e-01 6.27600e-02 -H5 H5 0.0000 0.0000 A 2.42146e-01 6.27600e-02 -HO HO 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -HS HS 0.0000 0.0000 A 1.06908e-01 6.56888e-02 -HW HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -HP HP 0.0000 0.0000 A 1.95998e-01 6.56888e-02 -I I 0.0000 0.0000 A 4.18722e-01 1.67360e+00 -Cl Cl 0.0000 0.0000 A 4.40104e-01 4.18400e-01 -Na Na 0.0000 0.0000 A 3.32840e-01 1.15897e-02 -IB IB 0.0000 0.0000 A 8.90899e-01 4.18400e-01 -MG Mg 0.0000 0.0000 A 1.41225e-01 3.74342e+00 -N N 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -NA NA 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -NB NB 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -NC NC 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -N2 N2 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -N3 N3 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -N* N* 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -O O 0.0000 0.0000 A 2.95992e-01 8.78640e-01 -OW OW 0.0000 0.0000 A 3.15061e-01 6.36386e-01 -OH OH 0.0000 0.0000 A 3.06647e-01 8.80314e-01 -OS OS 0.0000 0.0000 A 3.00001e-01 7.11280e-01 -O2 O2 0.0000 0.0000 A 2.95992e-01 8.78640e-01 -P P 0.0000 0.0000 A 3.74177e-01 8.36800e-01 -S S 0.0000 0.0000 A 3.56359e-01 1.04600e+00 -SH SH 0.0000 0.0000 A 3.56359e-01 1.04600e+00 -CU CU 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -FE FE 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -K K 0.0000 0.0000 A 4.73602e-01 1.37235e-03 -Rb Rb 0.0000 0.0000 A 5.26699e-01 7.11280e-04 -Cs Cs 0.0000 0.0000 A 6.04920e-01 3.37230e-04 -; spc water - use only with spc.itp & settles -OW_spc OW 0.0000 0.0000 A 3.16557e-01 6.50629e-01 -HW_spc HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -Li Li 0.0000 0.0000 A 2.02590e-01 7.65672e-02 -Zn Zn 0.0000 0.0000 A 1.95998e-01 5.23000e-02 -;tip4p-EW -HW_tip4pew HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -OW_tip4pew OW 0.0000 0.0000 A 3.16435e-01 6.80946e-01 -; tip4p -HW_tip4p HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -OW_tip4p OW 0.0000 0.0000 A 3.15365e-01 6.48520e-01 -;tip5p -HW_tip5p HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -OW_tip5p OW 0.0000 0.0000 A 3.12000e-01 6.69440e-01 -;tip3p heavy -HW_tip3p HW 4.0320 0.0000 A 0.00000e+00 0.00000e+00 -OW_tip3p OW 9.9520 0.0000 A 3.15061e-01 6.36386e-01 -; dummy defs -; MW=Dummy mass for tip4p/EW/5p water extra point charge -MW MW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -; Dummy masses for rigid CH3 and NH3 groups -MCH3 MCH3 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -MNH3 MNH3 0.0000 0.0000 A 0.00000e+00 0.00000e+00 +[ atomtypes ] +; name at.num mass charge ptype sigma epsilon +Br 35 79.90 0.0000 A 0.00000e+00 0.00000e+00 +C 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CA 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CB 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CC 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CK 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CM 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CN 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CQ 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CR 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CT 6 12.01 0.0000 A 3.39967e-01 4.57730e-01 +CV 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CW 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +C* 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +C0 20 40.08 0.0000 A 3.05240e-01 1.92376e+00 +F 9 19.00 0.0000 A 3.11815e-01 2.55224e-01 +H 1 1.008 0.0000 A 1.06908e-01 6.56888e-02 +HC 1 1.008 0.0000 A 2.64953e-01 6.56888e-02 +H1 1 1.008 0.0000 A 2.47135e-01 6.56888e-02 +H2 1 1.008 0.0000 A 2.29317e-01 6.56888e-02 +H3 1 1.008 0.0000 A 2.11499e-01 6.56888e-02 +HA 1 1.008 0.0000 A 2.59964e-01 6.27600e-02 +H4 1 1.008 0.0000 A 2.51055e-01 6.27600e-02 +H5 1 1.008 0.0000 A 2.42146e-01 6.27600e-02 +HO 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +HS 1 1.008 0.0000 A 1.06908e-01 6.56888e-02 +HW 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +HP 1 1.008 0.0000 A 1.95998e-01 6.56888e-02 +I 53 126.9 0.0000 A 4.18722e-01 1.67360e+00 +Cl 17 35.45 0.0000 A 4.40104e-01 4.18400e-01 +Na 11 22.99 0.0000 A 3.32840e-01 1.15897e-02 +IB 0 131.0 0.0000 A 8.90899e-01 4.18400e-01 +MG 12 24.305 0.0000 A 1.41225e-01 3.74342e+00 +N 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +NA 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +NB 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +NC 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +N2 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +N3 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +N* 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +O 8 16.00 0.0000 A 2.95992e-01 8.78640e-01 +OW 8 16.00 0.0000 A 3.15061e-01 6.36386e-01 +OH 8 16.00 0.0000 A 3.06647e-01 8.80314e-01 +OS 8 16.00 0.0000 A 3.00001e-01 7.11280e-01 +O2 8 16.00 0.0000 A 2.95992e-01 8.78640e-01 +P 15 30.97 0.0000 A 3.74177e-01 8.36800e-01 +S 16 32.06 0.0000 A 3.56359e-01 1.04600e+00 +SH 16 32.06 0.0000 A 3.56359e-01 1.04600e+00 +CU 29 63.55 0.0000 A 3.39967e-01 3.59824e-01 +FE 26 55.00 0.0000 A 0.00000e+00 0.00000e+00 +K 19 39.10 0.0000 A 4.73602e-01 1.37235e-03 +Rb 37 85.47 0.0000 A 5.26699e-01 7.11280e-04 +Cs 55 132.91 0.0000 A 6.04920e-01 3.37230e-04 +; spc water - use only with spc.itp & settles +OW_spc 8 15.9994 0.0000 A 3.16557e-01 6.50629e-01 +HW_spc 1 1.0080 0.0000 A 0.00000e+00 0.00000e+00 +Li 3 6.94 0.0000 A 2.02590e-01 7.65672e-02 +Zn 30 65.4 0.0000 A 1.95998e-01 5.23000e-02 +;tip4p-EW +HW_tip4pew 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +OW_tip4pew 8 16.00 0.0000 A 3.16435e-01 6.80946e-01 +; tip4p +HW_tip4p 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +OW_tip4p 8 16.00 0.0000 A 3.15365e-01 6.48520e-01 +;tip5p +HW_tip5p 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +OW_tip5p 8 16.00 0.0000 A 3.12000e-01 6.69440e-01 +; dummy defs +; MW=Dummy mass for tip4p/EW/5p water extra point charge +MW 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 +; Dummy masses for rigid CH3 and NH3 groups +MCH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 +MNH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 diff --git a/share/top/amber96.ff/atomtypes.atp b/share/top/amber96.ff/atomtypes.atp dissimilarity index 87% index 1edd14f6ae..a31392919a 100644 --- a/share/top/amber96.ff/atomtypes.atp +++ b/share/top/amber96.ff/atomtypes.atp @@ -1,68 +1,66 @@ -Br 79.90000 ; BR bromine -C 12.01000 ; C sp2 C carbonyl group -CA 12.01000 ; CA sp2 C pure aromatic (benzene) -CB 12.01000 ; CB sp2 aromatic C, 5&6 membered ring junction -CC 12.01000 ; CC sp2 aromatic C, 5 memb. ring HIS -CK 12.01000 ; CK sp2 C 5 memb.ring in purines -CM 12.01000 ; CM sp2 C pyrimidines in pos. 5 & 6 -CN 12.01000 ; CN sp2 C aromatic 5&6 memb.ring junct.(TRP) -CQ 12.01000 ; CQ sp2 C in 5 mem.ring of purines between 2 N -CR 12.01000 ; CR sp2 arom as CQ but in HIS -CT 12.01000 ; CT sp3 aliphatic C -CV 12.01000 ; CV sp2 arom. 5 memb.ring w/1 N and 1 H (HIS) -CW 12.01000 ; CW sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS) -C* 12.01000 ; C* sp2 arom. 5 memb.ring w/1 subst. (TRP) -C0 40.08000 ; Ca2+ calcium -F 19.00000 ; F fluorine -H 1.00800 ; H H bonded to nitrogen atoms -HC 1.00800 ; HC H aliph. bond. to C without electrwd.group -H1 1.00800 ; H1 H aliph. bond. to C with 1 electrwd. group -H2 1.00800 ; H2 H aliph. bond. to C with 2 electrwd.groups -H3 1.00800 ; H3 H aliph. bond. to C with 3 eletrwd.groups -HA 1.00800 ; HA H arom. bond. to C without elctrwd. groups -H4 1.00800 ; H4 H arom. bond. to C with 1 electrwd. group -H5 1.00800 ; H5 H arom. bond. to C with 2 electrwd. groups -HO 1.00800 ; HO hydroxyl group -HS 1.00800 ; HS hydrogen bonded to sulphur -HW 1.00800 ; HW H in TIP3P water -HP 1.00800 ; HP H bonded to C next to positively charged gr -I 126.90000 ; I iodine -Cl 35.45000 ; Cl- -Na 22.99000 ; Na+ -IB 131.00000 ; IB 'big ion w/ waters' for vacuum (Na+, 6H2O) -MG 24.30000 ; Mg2+ magnesium -N 14.01000 ; N sp2 nitrogen in amide groups -NA 14.01000 ; NA sp2 N in 5 memb.ring w/H atom (HIS) -NB 14.01000 ; NB sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) -NC 14.01000 ; NC sp2 N in 6 memb.ring w/LP (ADE,GUA) -N2 14.01000 ; N2 sp2 N in amino groups -N3 14.01000 ; N3 sp3 N for charged amino groups (Lys, etc) -N* 14.01000 ; N* sp2 N -O 16.00000 ; O carbonyl group oxygen -OW 16.00000 ; OW oxygen in TIP3P water -OH 16.00000 ; OH oxygen in hydroxyl group -OS 16.00000 ; OS ether and ester oxygen -O2 16.00000 ; O2 carboxyl and phosphate group oxygen -P 30.97000 ; P phosphate -S 32.06000 ; S sulphur in disulfide linkage -SH 32.06000 ; SH sulphur in cystine -CU 63.55000 ; CU copper -FE 55.00000 ; FE iron -K 39.10000 ; K+ potassium -Rb 85.47000 ; Rb+ rubidium -Cs 132.90000 ; Cs+ cesium -OW_spc 15.99940 ; SPC Water OW -HW_spc 1.00800 ; SPC Water HW -Li 6.94000 ; Li+ from parm94/96 -Zn 65.40000 ; Zn2+ from parm99 -HW_tip4pew 1.00800 ; tip4pEW HW -OW_tip4pew 16.00000 ; tip4pEW OW -HW_tip4p 1.00800 ; tip4p HW -OW_tip4p 16.00000 ; tip4p OW -HW_tip5p 1.00800 ; tip5p HW -OW_tip5p 16.00000 ; tip5p OW -HW_tip3p 4.03200 ; TIP3P HEAVY dummy water HW -OW_tip3p 9.95200 ; TIP3P heavy dummy water OW -MW 0.00000 ; Dummy mass for tip4p/5p water extra point charge -MCH3 0.00000 ; Dummy mass in rigid tetrahedral CH3 group -MNH3 0.00000 ; Dummy mass in rigid tetrahedral NH3 group +Br 79.90000 ; bromine +C 12.01000 ; sp2 C carbonyl group +CA 12.01000 ; sp2 C pure aromatic (benzene) +CB 12.01000 ; sp2 aromatic C, 5&6 membered ring junction +CC 12.01000 ; sp2 aromatic C, 5 memb. ring HIS +CK 12.01000 ; sp2 C 5 memb.ring in purines +CM 12.01000 ; sp2 C pyrimidines in pos. 5 & 6 +CN 12.01000 ; sp2 C aromatic 5&6 memb.ring junct.(TRP) +CQ 12.01000 ; sp2 C in 5 mem.ring of purines between 2 N +CR 12.01000 ; sp2 arom as CQ but in HIS +CT 12.01000 ; sp3 aliphatic C +CV 12.01000 ; sp2 arom. 5 memb.ring w/1 N and 1 H (HIS) +CW 12.01000 ; sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS) +C* 12.01000 ; sp2 arom. 5 memb.ring w/1 subst. (TRP) +C0 40.08000 ; calcium +F 19.00000 ; fluorine +H 1.00800 ; H bonded to nitrogen atoms +HC 1.00800 ; H aliph. bond. to C without electrwd.group +H1 1.00800 ; H aliph. bond. to C with 1 electrwd. group +H2 1.00800 ; H aliph. bond. to C with 2 electrwd.groups +H3 1.00800 ; H aliph. bond. to C with 3 eletrwd.groups +HA 1.00800 ; H arom. bond. to C without elctrwd. groups +H4 1.00800 ; H arom. bond. to C with 1 electrwd. group +H5 1.00800 ; H arom. bond. to C with 2 electrwd. groups +HO 1.00800 ; hydroxyl group +HS 1.00800 ; hydrogen bonded to sulphur (pol?) +HW 1.00800 ; H in TIP3P water +HP 1.00800 ; H bonded to C next to positively charged gr +I 126.90000 ; iodine (Applequist) +Cl 35.45000 ; chlorine (Applequist) +Na 22.99000 ; Na+, ions pol:J.PhysC,11,1541,(1978) +IB 131.00000 ; 'big ion w/ waters' for vacuum (Na+, 6H2O) +MG 24.30500 ; magnesium +N 14.01000 ; sp2 nitrogen in amide groups +NA 14.01000 ; sp2 N in 5 memb.ring w/H atom (HIS) +NB 14.01000 ; sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) +NC 14.01000 ; sp2 N in 6 memb.ring w/LP (ADE,GUA) +N2 14.01000 ; sp2 N in amino groups +N3 14.01000 ; sp3 N for charged amino groups (Lys, etc) +N* 14.01000 ; sp2 N +O 16.00000 ; carbonyl group oxygen +OW 16.00000 ; oxygen in TIP3P water +OH 16.00000 ; oxygen in hydroxyl group +OS 16.00000 ; ether and ester oxygen +O2 16.00000 ; carboxyl and phosphate group oxygen +P 30.97000 ; phosphate,pol:JACS,112,8543,90,K.J.Miller +S 32.06000 ; S in disulfide linkage,pol:JPC,102,2399,98 +SH 32.06000 ; S in cystine +CU 63.55000 ; copper +FE 55.00000 ; iron +K 39.10000 ; potassium +Rb 85.47000 ; rubidium +Cs 132.90000 ; cesium +OW_spc 15.99940 ; SPC Water OW +HW_spc 1.00800 ; SPC Water HW +Li 6.94000 ; lithium, ions pol:J.PhysC,11,1541,(1978) +Zn 65.40000 ; Zn2+ +HW_tip4pew 1.00800 ; tip4pEW HW +OW_tip4pew 16.00000 ; tip4pEW OW +HW_tip4p 1.00800 ; tip4p HW +OW_tip4p 16.00000 ; tip4p OW +HW_tip5p 1.00800 ; tip5p HW +OW_tip5p 16.00000 ; tip5p OW +MW 0.00000 ; Virtual site for tip4p/5p water point charge +MCH3 0.00000 ; Dummy mass in rigid tetrahedral CH3 group +MNH3 0.00000 ; Dummy mass in rigid tetrahedral NH3 group diff --git a/share/top/amber96.ff/ffnonbonded.itp b/share/top/amber96.ff/ffnonbonded.itp dissimilarity index 93% index 7dd6009240..ef3fde6d98 100644 --- a/share/top/amber96.ff/ffnonbonded.itp +++ b/share/top/amber96.ff/ffnonbonded.itp @@ -1,78 +1,75 @@ -[ atomtypes ] -; name bond_type mass charge ptype sigma epsilon -Br BR 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -C C 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CA CA 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CB CB 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CC CC 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CK CK 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CM CM 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CN CN 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CQ CQ 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CR CR 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CT CT 0.0000 0.0000 A 3.39967e-01 4.57730e-01 -CV CV 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CW CW 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -C* C* 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -C0 Ca 0.0000 0.0000 A 3.05240e-01 1.92376e+00 -F F 0.0000 0.0000 A 3.11815e-01 2.55224e-01 -H H 0.0000 0.0000 A 1.06908e-01 6.56888e-02 -HC HC 0.0000 0.0000 A 2.64953e-01 6.56888e-02 -H1 H1 0.0000 0.0000 A 2.47135e-01 6.56888e-02 -H2 H2 0.0000 0.0000 A 2.29317e-01 6.56888e-02 -H3 H3 0.0000 0.0000 A 2.11499e-01 6.56888e-02 -HA HA 0.0000 0.0000 A 2.59964e-01 6.27600e-02 -H4 H4 0.0000 0.0000 A 2.51055e-01 6.27600e-02 -H5 H5 0.0000 0.0000 A 2.42146e-01 6.27600e-02 -HO HO 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -HS HS 0.0000 0.0000 A 1.06908e-01 6.56888e-02 -HW HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -HP HP 0.0000 0.0000 A 1.95998e-01 6.56888e-02 -I I 0.0000 0.0000 A 4.18722e-01 1.67360e+00 -Cl Cl 0.0000 0.0000 A 4.40104e-01 4.18400e-01 -Na Na 0.0000 0.0000 A 3.32840e-01 1.15897e-02 -IB IB 0.0000 0.0000 A 8.90899e-01 4.18400e-01 -MG Mg 0.0000 0.0000 A 1.41225e-01 3.74342e+00 -N N 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -NA NA 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -NB NB 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -NC NC 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -N2 N2 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -N3 N3 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -N* N* 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -O O 0.0000 0.0000 A 2.95992e-01 8.78640e-01 -OW OW 0.0000 0.0000 A 3.15061e-01 6.36386e-01 -OH OH 0.0000 0.0000 A 3.06647e-01 8.80314e-01 -OS OS 0.0000 0.0000 A 3.00001e-01 7.11280e-01 -O2 O2 0.0000 0.0000 A 2.95992e-01 8.78640e-01 -P P 0.0000 0.0000 A 3.74177e-01 8.36800e-01 -S S 0.0000 0.0000 A 3.56359e-01 1.04600e+00 -SH SH 0.0000 0.0000 A 3.56359e-01 1.04600e+00 -CU CU 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -FE FE 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -K K 0.0000 0.0000 A 4.73602e-01 1.37235e-03 -Rb Rb 0.0000 0.0000 A 5.26699e-01 7.11280e-04 -Cs Cs 0.0000 0.0000 A 6.04920e-01 3.37230e-04 -; spc water - use only with spc.itp & settles -OW_spc OW 0.0000 0.0000 A 3.16557e-01 6.50629e-01 -HW_spc HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -Li Li 0.0000 0.0000 A 2.02590e-01 7.65672e-02 -Zn Zn 0.0000 0.0000 A 1.95998e-01 5.23000e-02 -;tip4p-EW -HW_tip4pew HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -OW_tip4pew OW 0.0000 0.0000 A 3.16435e-01 6.80946e-01 -; tip4p -HW_tip4p HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -OW_tip4p OW 0.0000 0.0000 A 3.15365e-01 6.48520e-01 -;tip5p -HW_tip5p HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -OW_tip5p OW 0.0000 0.0000 A 3.12000e-01 6.69440e-01 -;tip3p heavy -HW_tip3p HW 4.0320 0.0000 A 0.00000e+00 0.00000e+00 -OW_tip3p OW 9.9520 0.0000 A 3.15061e-01 6.36386e-01 -; dummy defs -; MW=Dummy mass for tip4p/EW/5p water extra point charge -MW MW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -; Dummy masses for rigid CH3 and NH3 groups -MCH3 MCH3 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -MNH3 MNH3 0.0000 0.0000 A 0.00000e+00 0.00000e+00 +[ atomtypes ] +; name at.num mass charge ptype sigma epsilon +Br 35 79.90 0.0000 A 0.00000e+00 0.00000e+00 +C 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CA 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CB 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CC 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CK 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CM 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CN 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CQ 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CR 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CT 6 12.01 0.0000 A 3.39967e-01 4.57730e-01 +CV 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CW 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +C* 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +C0 20 40.08 0.0000 A 3.05240e-01 1.92376e+00 +F 9 19.00 0.0000 A 3.11815e-01 2.55224e-01 +H 1 1.008 0.0000 A 1.06908e-01 6.56888e-02 +HC 1 1.008 0.0000 A 2.64953e-01 6.56888e-02 +H1 1 1.008 0.0000 A 2.47135e-01 6.56888e-02 +H2 1 1.008 0.0000 A 2.29317e-01 6.56888e-02 +H3 1 1.008 0.0000 A 2.11499e-01 6.56888e-02 +HA 1 1.008 0.0000 A 2.59964e-01 6.27600e-02 +H4 1 1.008 0.0000 A 2.51055e-01 6.27600e-02 +H5 1 1.008 0.0000 A 2.42146e-01 6.27600e-02 +HO 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +HS 1 1.008 0.0000 A 1.06908e-01 6.56888e-02 +HW 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +HP 1 1.008 0.0000 A 1.95998e-01 6.56888e-02 +I 53 126.9 0.0000 A 4.18722e-01 1.67360e+00 +Cl 17 35.45 0.0000 A 4.40104e-01 4.18400e-01 +Na 11 22.99 0.0000 A 3.32840e-01 1.15897e-02 +IB 0 131.0 0.0000 A 8.90899e-01 4.18400e-01 +MG 12 24.305 0.0000 A 1.41225e-01 3.74342e+00 +N 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +NA 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +NB 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +NC 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +N2 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +N3 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +N* 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +O 8 16.00 0.0000 A 2.95992e-01 8.78640e-01 +OW 8 16.00 0.0000 A 3.15061e-01 6.36386e-01 +OH 8 16.00 0.0000 A 3.06647e-01 8.80314e-01 +OS 8 16.00 0.0000 A 3.00001e-01 7.11280e-01 +O2 8 16.00 0.0000 A 2.95992e-01 8.78640e-01 +P 15 30.97 0.0000 A 3.74177e-01 8.36800e-01 +S 16 32.06 0.0000 A 3.56359e-01 1.04600e+00 +SH 16 32.06 0.0000 A 3.56359e-01 1.04600e+00 +CU 29 63.55 0.0000 A 3.39967e-01 3.59824e-01 +FE 26 55.00 0.0000 A 0.00000e+00 0.00000e+00 +K 19 39.10 0.0000 A 4.73602e-01 1.37235e-03 +Rb 37 85.47 0.0000 A 5.26699e-01 7.11280e-04 +Cs 55 132.91 0.0000 A 6.04920e-01 3.37230e-04 +; spc water - use only with spc.itp & settles +OW_spc 8 15.9994 0.0000 A 3.16557e-01 6.50629e-01 +HW_spc 1 1.0080 0.0000 A 0.00000e+00 0.00000e+00 +Li 3 6.94 0.0000 A 2.02590e-01 7.65672e-02 +Zn 30 65.4 0.0000 A 1.95998e-01 5.23000e-02 +;tip4p-EW +HW_tip4pew 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +OW_tip4pew 8 16.00 0.0000 A 3.16435e-01 6.80946e-01 +; tip4p +HW_tip4p 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +OW_tip4p 8 16.00 0.0000 A 3.15365e-01 6.48520e-01 +;tip5p +HW_tip5p 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +OW_tip5p 8 16.00 0.0000 A 3.12000e-01 6.69440e-01 +; dummy defs +; MW=Dummy mass for tip4p/EW/5p water extra point charge +MW 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 +; Dummy masses for rigid CH3 and NH3 groups +MCH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 +MNH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 diff --git a/share/top/amber99.ff/atomtypes.atp b/share/top/amber99.ff/atomtypes.atp dissimilarity index 87% index 1edd14f6ae..a31392919a 100644 --- a/share/top/amber99.ff/atomtypes.atp +++ b/share/top/amber99.ff/atomtypes.atp @@ -1,68 +1,66 @@ -Br 79.90000 ; BR bromine -C 12.01000 ; C sp2 C carbonyl group -CA 12.01000 ; CA sp2 C pure aromatic (benzene) -CB 12.01000 ; CB sp2 aromatic C, 5&6 membered ring junction -CC 12.01000 ; CC sp2 aromatic C, 5 memb. ring HIS -CK 12.01000 ; CK sp2 C 5 memb.ring in purines -CM 12.01000 ; CM sp2 C pyrimidines in pos. 5 & 6 -CN 12.01000 ; CN sp2 C aromatic 5&6 memb.ring junct.(TRP) -CQ 12.01000 ; CQ sp2 C in 5 mem.ring of purines between 2 N -CR 12.01000 ; CR sp2 arom as CQ but in HIS -CT 12.01000 ; CT sp3 aliphatic C -CV 12.01000 ; CV sp2 arom. 5 memb.ring w/1 N and 1 H (HIS) -CW 12.01000 ; CW sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS) -C* 12.01000 ; C* sp2 arom. 5 memb.ring w/1 subst. (TRP) -C0 40.08000 ; Ca2+ calcium -F 19.00000 ; F fluorine -H 1.00800 ; H H bonded to nitrogen atoms -HC 1.00800 ; HC H aliph. bond. to C without electrwd.group -H1 1.00800 ; H1 H aliph. bond. to C with 1 electrwd. group -H2 1.00800 ; H2 H aliph. bond. to C with 2 electrwd.groups -H3 1.00800 ; H3 H aliph. bond. to C with 3 eletrwd.groups -HA 1.00800 ; HA H arom. bond. to C without elctrwd. groups -H4 1.00800 ; H4 H arom. bond. to C with 1 electrwd. group -H5 1.00800 ; H5 H arom. bond. to C with 2 electrwd. groups -HO 1.00800 ; HO hydroxyl group -HS 1.00800 ; HS hydrogen bonded to sulphur -HW 1.00800 ; HW H in TIP3P water -HP 1.00800 ; HP H bonded to C next to positively charged gr -I 126.90000 ; I iodine -Cl 35.45000 ; Cl- -Na 22.99000 ; Na+ -IB 131.00000 ; IB 'big ion w/ waters' for vacuum (Na+, 6H2O) -MG 24.30000 ; Mg2+ magnesium -N 14.01000 ; N sp2 nitrogen in amide groups -NA 14.01000 ; NA sp2 N in 5 memb.ring w/H atom (HIS) -NB 14.01000 ; NB sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) -NC 14.01000 ; NC sp2 N in 6 memb.ring w/LP (ADE,GUA) -N2 14.01000 ; N2 sp2 N in amino groups -N3 14.01000 ; N3 sp3 N for charged amino groups (Lys, etc) -N* 14.01000 ; N* sp2 N -O 16.00000 ; O carbonyl group oxygen -OW 16.00000 ; OW oxygen in TIP3P water -OH 16.00000 ; OH oxygen in hydroxyl group -OS 16.00000 ; OS ether and ester oxygen -O2 16.00000 ; O2 carboxyl and phosphate group oxygen -P 30.97000 ; P phosphate -S 32.06000 ; S sulphur in disulfide linkage -SH 32.06000 ; SH sulphur in cystine -CU 63.55000 ; CU copper -FE 55.00000 ; FE iron -K 39.10000 ; K+ potassium -Rb 85.47000 ; Rb+ rubidium -Cs 132.90000 ; Cs+ cesium -OW_spc 15.99940 ; SPC Water OW -HW_spc 1.00800 ; SPC Water HW -Li 6.94000 ; Li+ from parm94/96 -Zn 65.40000 ; Zn2+ from parm99 -HW_tip4pew 1.00800 ; tip4pEW HW -OW_tip4pew 16.00000 ; tip4pEW OW -HW_tip4p 1.00800 ; tip4p HW -OW_tip4p 16.00000 ; tip4p OW -HW_tip5p 1.00800 ; tip5p HW -OW_tip5p 16.00000 ; tip5p OW -HW_tip3p 4.03200 ; TIP3P HEAVY dummy water HW -OW_tip3p 9.95200 ; TIP3P heavy dummy water OW -MW 0.00000 ; Dummy mass for tip4p/5p water extra point charge -MCH3 0.00000 ; Dummy mass in rigid tetrahedral CH3 group -MNH3 0.00000 ; Dummy mass in rigid tetrahedral NH3 group +Br 79.90000 ; bromine +C 12.01000 ; sp2 C carbonyl group +CA 12.01000 ; sp2 C pure aromatic (benzene) +CB 12.01000 ; sp2 aromatic C, 5&6 membered ring junction +CC 12.01000 ; sp2 aromatic C, 5 memb. ring HIS +CK 12.01000 ; sp2 C 5 memb.ring in purines +CM 12.01000 ; sp2 C pyrimidines in pos. 5 & 6 +CN 12.01000 ; sp2 C aromatic 5&6 memb.ring junct.(TRP) +CQ 12.01000 ; sp2 C in 5 mem.ring of purines between 2 N +CR 12.01000 ; sp2 arom as CQ but in HIS +CT 12.01000 ; sp3 aliphatic C +CV 12.01000 ; sp2 arom. 5 memb.ring w/1 N and 1 H (HIS) +CW 12.01000 ; sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS) +C* 12.01000 ; sp2 arom. 5 memb.ring w/1 subst. (TRP) +C0 40.08000 ; calcium +F 19.00000 ; fluorine +H 1.00800 ; H bonded to nitrogen atoms +HC 1.00800 ; H aliph. bond. to C without electrwd.group +H1 1.00800 ; H aliph. bond. to C with 1 electrwd. group +H2 1.00800 ; H aliph. bond. to C with 2 electrwd.groups +H3 1.00800 ; H aliph. bond. to C with 3 eletrwd.groups +HA 1.00800 ; H arom. bond. to C without elctrwd. groups +H4 1.00800 ; H arom. bond. to C with 1 electrwd. group +H5 1.00800 ; H arom. bond. to C with 2 electrwd. groups +HO 1.00800 ; hydroxyl group +HS 1.00800 ; hydrogen bonded to sulphur (pol?) +HW 1.00800 ; H in TIP3P water +HP 1.00800 ; H bonded to C next to positively charged gr +I 126.90000 ; iodine (Applequist) +Cl 35.45000 ; chlorine (Applequist) +Na 22.99000 ; Na+, ions pol:J.PhysC,11,1541,(1978) +IB 131.00000 ; 'big ion w/ waters' for vacuum (Na+, 6H2O) +MG 24.30500 ; magnesium +N 14.01000 ; sp2 nitrogen in amide groups +NA 14.01000 ; sp2 N in 5 memb.ring w/H atom (HIS) +NB 14.01000 ; sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) +NC 14.01000 ; sp2 N in 6 memb.ring w/LP (ADE,GUA) +N2 14.01000 ; sp2 N in amino groups +N3 14.01000 ; sp3 N for charged amino groups (Lys, etc) +N* 14.01000 ; sp2 N +O 16.00000 ; carbonyl group oxygen +OW 16.00000 ; oxygen in TIP3P water +OH 16.00000 ; oxygen in hydroxyl group +OS 16.00000 ; ether and ester oxygen +O2 16.00000 ; carboxyl and phosphate group oxygen +P 30.97000 ; phosphate,pol:JACS,112,8543,90,K.J.Miller +S 32.06000 ; S in disulfide linkage,pol:JPC,102,2399,98 +SH 32.06000 ; S in cystine +CU 63.55000 ; copper +FE 55.00000 ; iron +K 39.10000 ; potassium +Rb 85.47000 ; rubidium +Cs 132.90000 ; cesium +OW_spc 15.99940 ; SPC Water OW +HW_spc 1.00800 ; SPC Water HW +Li 6.94000 ; lithium, ions pol:J.PhysC,11,1541,(1978) +Zn 65.40000 ; Zn2+ +HW_tip4pew 1.00800 ; tip4pEW HW +OW_tip4pew 16.00000 ; tip4pEW OW +HW_tip4p 1.00800 ; tip4p HW +OW_tip4p 16.00000 ; tip4p OW +HW_tip5p 1.00800 ; tip5p HW +OW_tip5p 16.00000 ; tip5p OW +MW 0.00000 ; Virtual site for tip4p/5p water point charge +MCH3 0.00000 ; Dummy mass in rigid tetrahedral CH3 group +MNH3 0.00000 ; Dummy mass in rigid tetrahedral NH3 group diff --git a/share/top/amber99.ff/ffnonbonded.itp b/share/top/amber99.ff/ffnonbonded.itp dissimilarity index 93% index 7dd6009240..ef3fde6d98 100644 --- a/share/top/amber99.ff/ffnonbonded.itp +++ b/share/top/amber99.ff/ffnonbonded.itp @@ -1,78 +1,75 @@ -[ atomtypes ] -; name bond_type mass charge ptype sigma epsilon -Br BR 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -C C 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CA CA 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CB CB 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CC CC 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CK CK 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CM CM 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CN CN 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CQ CQ 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CR CR 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CT CT 0.0000 0.0000 A 3.39967e-01 4.57730e-01 -CV CV 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CW CW 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -C* C* 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -C0 Ca 0.0000 0.0000 A 3.05240e-01 1.92376e+00 -F F 0.0000 0.0000 A 3.11815e-01 2.55224e-01 -H H 0.0000 0.0000 A 1.06908e-01 6.56888e-02 -HC HC 0.0000 0.0000 A 2.64953e-01 6.56888e-02 -H1 H1 0.0000 0.0000 A 2.47135e-01 6.56888e-02 -H2 H2 0.0000 0.0000 A 2.29317e-01 6.56888e-02 -H3 H3 0.0000 0.0000 A 2.11499e-01 6.56888e-02 -HA HA 0.0000 0.0000 A 2.59964e-01 6.27600e-02 -H4 H4 0.0000 0.0000 A 2.51055e-01 6.27600e-02 -H5 H5 0.0000 0.0000 A 2.42146e-01 6.27600e-02 -HO HO 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -HS HS 0.0000 0.0000 A 1.06908e-01 6.56888e-02 -HW HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -HP HP 0.0000 0.0000 A 1.95998e-01 6.56888e-02 -I I 0.0000 0.0000 A 4.18722e-01 1.67360e+00 -Cl Cl 0.0000 0.0000 A 4.40104e-01 4.18400e-01 -Na Na 0.0000 0.0000 A 3.32840e-01 1.15897e-02 -IB IB 0.0000 0.0000 A 8.90899e-01 4.18400e-01 -MG Mg 0.0000 0.0000 A 1.41225e-01 3.74342e+00 -N N 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -NA NA 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -NB NB 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -NC NC 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -N2 N2 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -N3 N3 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -N* N* 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -O O 0.0000 0.0000 A 2.95992e-01 8.78640e-01 -OW OW 0.0000 0.0000 A 3.15061e-01 6.36386e-01 -OH OH 0.0000 0.0000 A 3.06647e-01 8.80314e-01 -OS OS 0.0000 0.0000 A 3.00001e-01 7.11280e-01 -O2 O2 0.0000 0.0000 A 2.95992e-01 8.78640e-01 -P P 0.0000 0.0000 A 3.74177e-01 8.36800e-01 -S S 0.0000 0.0000 A 3.56359e-01 1.04600e+00 -SH SH 0.0000 0.0000 A 3.56359e-01 1.04600e+00 -CU CU 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -FE FE 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -K K 0.0000 0.0000 A 4.73602e-01 1.37235e-03 -Rb Rb 0.0000 0.0000 A 5.26699e-01 7.11280e-04 -Cs Cs 0.0000 0.0000 A 6.04920e-01 3.37230e-04 -; spc water - use only with spc.itp & settles -OW_spc OW 0.0000 0.0000 A 3.16557e-01 6.50629e-01 -HW_spc HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -Li Li 0.0000 0.0000 A 2.02590e-01 7.65672e-02 -Zn Zn 0.0000 0.0000 A 1.95998e-01 5.23000e-02 -;tip4p-EW -HW_tip4pew HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -OW_tip4pew OW 0.0000 0.0000 A 3.16435e-01 6.80946e-01 -; tip4p -HW_tip4p HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -OW_tip4p OW 0.0000 0.0000 A 3.15365e-01 6.48520e-01 -;tip5p -HW_tip5p HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -OW_tip5p OW 0.0000 0.0000 A 3.12000e-01 6.69440e-01 -;tip3p heavy -HW_tip3p HW 4.0320 0.0000 A 0.00000e+00 0.00000e+00 -OW_tip3p OW 9.9520 0.0000 A 3.15061e-01 6.36386e-01 -; dummy defs -; MW=Dummy mass for tip4p/EW/5p water extra point charge -MW MW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -; Dummy masses for rigid CH3 and NH3 groups -MCH3 MCH3 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -MNH3 MNH3 0.0000 0.0000 A 0.00000e+00 0.00000e+00 +[ atomtypes ] +; name at.num mass charge ptype sigma epsilon +Br 35 79.90 0.0000 A 0.00000e+00 0.00000e+00 +C 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CA 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CB 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CC 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CK 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CM 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CN 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CQ 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CR 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CT 6 12.01 0.0000 A 3.39967e-01 4.57730e-01 +CV 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CW 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +C* 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +C0 20 40.08 0.0000 A 3.05240e-01 1.92376e+00 +F 9 19.00 0.0000 A 3.11815e-01 2.55224e-01 +H 1 1.008 0.0000 A 1.06908e-01 6.56888e-02 +HC 1 1.008 0.0000 A 2.64953e-01 6.56888e-02 +H1 1 1.008 0.0000 A 2.47135e-01 6.56888e-02 +H2 1 1.008 0.0000 A 2.29317e-01 6.56888e-02 +H3 1 1.008 0.0000 A 2.11499e-01 6.56888e-02 +HA 1 1.008 0.0000 A 2.59964e-01 6.27600e-02 +H4 1 1.008 0.0000 A 2.51055e-01 6.27600e-02 +H5 1 1.008 0.0000 A 2.42146e-01 6.27600e-02 +HO 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +HS 1 1.008 0.0000 A 1.06908e-01 6.56888e-02 +HW 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +HP 1 1.008 0.0000 A 1.95998e-01 6.56888e-02 +I 53 126.9 0.0000 A 4.18722e-01 1.67360e+00 +Cl 17 35.45 0.0000 A 4.40104e-01 4.18400e-01 +Na 11 22.99 0.0000 A 3.32840e-01 1.15897e-02 +IB 0 131.0 0.0000 A 8.90899e-01 4.18400e-01 +MG 12 24.305 0.0000 A 1.41225e-01 3.74342e+00 +N 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +NA 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +NB 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +NC 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +N2 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +N3 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +N* 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +O 8 16.00 0.0000 A 2.95992e-01 8.78640e-01 +OW 8 16.00 0.0000 A 3.15061e-01 6.36386e-01 +OH 8 16.00 0.0000 A 3.06647e-01 8.80314e-01 +OS 8 16.00 0.0000 A 3.00001e-01 7.11280e-01 +O2 8 16.00 0.0000 A 2.95992e-01 8.78640e-01 +P 15 30.97 0.0000 A 3.74177e-01 8.36800e-01 +S 16 32.06 0.0000 A 3.56359e-01 1.04600e+00 +SH 16 32.06 0.0000 A 3.56359e-01 1.04600e+00 +CU 29 63.55 0.0000 A 3.39967e-01 3.59824e-01 +FE 26 55.00 0.0000 A 0.00000e+00 0.00000e+00 +K 19 39.10 0.0000 A 4.73602e-01 1.37235e-03 +Rb 37 85.47 0.0000 A 5.26699e-01 7.11280e-04 +Cs 55 132.91 0.0000 A 6.04920e-01 3.37230e-04 +; spc water - use only with spc.itp & settles +OW_spc 8 15.9994 0.0000 A 3.16557e-01 6.50629e-01 +HW_spc 1 1.0080 0.0000 A 0.00000e+00 0.00000e+00 +Li 3 6.94 0.0000 A 2.02590e-01 7.65672e-02 +Zn 30 65.4 0.0000 A 1.95998e-01 5.23000e-02 +;tip4p-EW +HW_tip4pew 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +OW_tip4pew 8 16.00 0.0000 A 3.16435e-01 6.80946e-01 +; tip4p +HW_tip4p 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +OW_tip4p 8 16.00 0.0000 A 3.15365e-01 6.48520e-01 +;tip5p +HW_tip5p 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +OW_tip5p 8 16.00 0.0000 A 3.12000e-01 6.69440e-01 +; dummy defs +; MW=Dummy mass for tip4p/EW/5p water extra point charge +MW 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 +; Dummy masses for rigid CH3 and NH3 groups +MCH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 +MNH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 diff --git a/share/top/amber99sb-ildn.ff/atomtypes.atp b/share/top/amber99sb-ildn.ff/atomtypes.atp dissimilarity index 87% index 1edd14f6ae..a31392919a 100644 --- a/share/top/amber99sb-ildn.ff/atomtypes.atp +++ b/share/top/amber99sb-ildn.ff/atomtypes.atp @@ -1,68 +1,66 @@ -Br 79.90000 ; BR bromine -C 12.01000 ; C sp2 C carbonyl group -CA 12.01000 ; CA sp2 C pure aromatic (benzene) -CB 12.01000 ; CB sp2 aromatic C, 5&6 membered ring junction -CC 12.01000 ; CC sp2 aromatic C, 5 memb. ring HIS -CK 12.01000 ; CK sp2 C 5 memb.ring in purines -CM 12.01000 ; CM sp2 C pyrimidines in pos. 5 & 6 -CN 12.01000 ; CN sp2 C aromatic 5&6 memb.ring junct.(TRP) -CQ 12.01000 ; CQ sp2 C in 5 mem.ring of purines between 2 N -CR 12.01000 ; CR sp2 arom as CQ but in HIS -CT 12.01000 ; CT sp3 aliphatic C -CV 12.01000 ; CV sp2 arom. 5 memb.ring w/1 N and 1 H (HIS) -CW 12.01000 ; CW sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS) -C* 12.01000 ; C* sp2 arom. 5 memb.ring w/1 subst. (TRP) -C0 40.08000 ; Ca2+ calcium -F 19.00000 ; F fluorine -H 1.00800 ; H H bonded to nitrogen atoms -HC 1.00800 ; HC H aliph. bond. to C without electrwd.group -H1 1.00800 ; H1 H aliph. bond. to C with 1 electrwd. group -H2 1.00800 ; H2 H aliph. bond. to C with 2 electrwd.groups -H3 1.00800 ; H3 H aliph. bond. to C with 3 eletrwd.groups -HA 1.00800 ; HA H arom. bond. to C without elctrwd. groups -H4 1.00800 ; H4 H arom. bond. to C with 1 electrwd. group -H5 1.00800 ; H5 H arom. bond. to C with 2 electrwd. groups -HO 1.00800 ; HO hydroxyl group -HS 1.00800 ; HS hydrogen bonded to sulphur -HW 1.00800 ; HW H in TIP3P water -HP 1.00800 ; HP H bonded to C next to positively charged gr -I 126.90000 ; I iodine -Cl 35.45000 ; Cl- -Na 22.99000 ; Na+ -IB 131.00000 ; IB 'big ion w/ waters' for vacuum (Na+, 6H2O) -MG 24.30000 ; Mg2+ magnesium -N 14.01000 ; N sp2 nitrogen in amide groups -NA 14.01000 ; NA sp2 N in 5 memb.ring w/H atom (HIS) -NB 14.01000 ; NB sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) -NC 14.01000 ; NC sp2 N in 6 memb.ring w/LP (ADE,GUA) -N2 14.01000 ; N2 sp2 N in amino groups -N3 14.01000 ; N3 sp3 N for charged amino groups (Lys, etc) -N* 14.01000 ; N* sp2 N -O 16.00000 ; O carbonyl group oxygen -OW 16.00000 ; OW oxygen in TIP3P water -OH 16.00000 ; OH oxygen in hydroxyl group -OS 16.00000 ; OS ether and ester oxygen -O2 16.00000 ; O2 carboxyl and phosphate group oxygen -P 30.97000 ; P phosphate -S 32.06000 ; S sulphur in disulfide linkage -SH 32.06000 ; SH sulphur in cystine -CU 63.55000 ; CU copper -FE 55.00000 ; FE iron -K 39.10000 ; K+ potassium -Rb 85.47000 ; Rb+ rubidium -Cs 132.90000 ; Cs+ cesium -OW_spc 15.99940 ; SPC Water OW -HW_spc 1.00800 ; SPC Water HW -Li 6.94000 ; Li+ from parm94/96 -Zn 65.40000 ; Zn2+ from parm99 -HW_tip4pew 1.00800 ; tip4pEW HW -OW_tip4pew 16.00000 ; tip4pEW OW -HW_tip4p 1.00800 ; tip4p HW -OW_tip4p 16.00000 ; tip4p OW -HW_tip5p 1.00800 ; tip5p HW -OW_tip5p 16.00000 ; tip5p OW -HW_tip3p 4.03200 ; TIP3P HEAVY dummy water HW -OW_tip3p 9.95200 ; TIP3P heavy dummy water OW -MW 0.00000 ; Dummy mass for tip4p/5p water extra point charge -MCH3 0.00000 ; Dummy mass in rigid tetrahedral CH3 group -MNH3 0.00000 ; Dummy mass in rigid tetrahedral NH3 group +Br 79.90000 ; bromine +C 12.01000 ; sp2 C carbonyl group +CA 12.01000 ; sp2 C pure aromatic (benzene) +CB 12.01000 ; sp2 aromatic C, 5&6 membered ring junction +CC 12.01000 ; sp2 aromatic C, 5 memb. ring HIS +CK 12.01000 ; sp2 C 5 memb.ring in purines +CM 12.01000 ; sp2 C pyrimidines in pos. 5 & 6 +CN 12.01000 ; sp2 C aromatic 5&6 memb.ring junct.(TRP) +CQ 12.01000 ; sp2 C in 5 mem.ring of purines between 2 N +CR 12.01000 ; sp2 arom as CQ but in HIS +CT 12.01000 ; sp3 aliphatic C +CV 12.01000 ; sp2 arom. 5 memb.ring w/1 N and 1 H (HIS) +CW 12.01000 ; sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS) +C* 12.01000 ; sp2 arom. 5 memb.ring w/1 subst. (TRP) +C0 40.08000 ; calcium +F 19.00000 ; fluorine +H 1.00800 ; H bonded to nitrogen atoms +HC 1.00800 ; H aliph. bond. to C without electrwd.group +H1 1.00800 ; H aliph. bond. to C with 1 electrwd. group +H2 1.00800 ; H aliph. bond. to C with 2 electrwd.groups +H3 1.00800 ; H aliph. bond. to C with 3 eletrwd.groups +HA 1.00800 ; H arom. bond. to C without elctrwd. groups +H4 1.00800 ; H arom. bond. to C with 1 electrwd. group +H5 1.00800 ; H arom. bond. to C with 2 electrwd. groups +HO 1.00800 ; hydroxyl group +HS 1.00800 ; hydrogen bonded to sulphur (pol?) +HW 1.00800 ; H in TIP3P water +HP 1.00800 ; H bonded to C next to positively charged gr +I 126.90000 ; iodine (Applequist) +Cl 35.45000 ; chlorine (Applequist) +Na 22.99000 ; Na+, ions pol:J.PhysC,11,1541,(1978) +IB 131.00000 ; 'big ion w/ waters' for vacuum (Na+, 6H2O) +MG 24.30500 ; magnesium +N 14.01000 ; sp2 nitrogen in amide groups +NA 14.01000 ; sp2 N in 5 memb.ring w/H atom (HIS) +NB 14.01000 ; sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) +NC 14.01000 ; sp2 N in 6 memb.ring w/LP (ADE,GUA) +N2 14.01000 ; sp2 N in amino groups +N3 14.01000 ; sp3 N for charged amino groups (Lys, etc) +N* 14.01000 ; sp2 N +O 16.00000 ; carbonyl group oxygen +OW 16.00000 ; oxygen in TIP3P water +OH 16.00000 ; oxygen in hydroxyl group +OS 16.00000 ; ether and ester oxygen +O2 16.00000 ; carboxyl and phosphate group oxygen +P 30.97000 ; phosphate,pol:JACS,112,8543,90,K.J.Miller +S 32.06000 ; S in disulfide linkage,pol:JPC,102,2399,98 +SH 32.06000 ; S in cystine +CU 63.55000 ; copper +FE 55.00000 ; iron +K 39.10000 ; potassium +Rb 85.47000 ; rubidium +Cs 132.90000 ; cesium +OW_spc 15.99940 ; SPC Water OW +HW_spc 1.00800 ; SPC Water HW +Li 6.94000 ; lithium, ions pol:J.PhysC,11,1541,(1978) +Zn 65.40000 ; Zn2+ +HW_tip4pew 1.00800 ; tip4pEW HW +OW_tip4pew 16.00000 ; tip4pEW OW +HW_tip4p 1.00800 ; tip4p HW +OW_tip4p 16.00000 ; tip4p OW +HW_tip5p 1.00800 ; tip5p HW +OW_tip5p 16.00000 ; tip5p OW +MW 0.00000 ; Virtual site for tip4p/5p water point charge +MCH3 0.00000 ; Dummy mass in rigid tetrahedral CH3 group +MNH3 0.00000 ; Dummy mass in rigid tetrahedral NH3 group diff --git a/share/top/amber99sb-ildn.ff/ffnonbonded.itp b/share/top/amber99sb-ildn.ff/ffnonbonded.itp dissimilarity index 93% index 7dd6009240..ef3fde6d98 100644 --- a/share/top/amber99sb-ildn.ff/ffnonbonded.itp +++ b/share/top/amber99sb-ildn.ff/ffnonbonded.itp @@ -1,78 +1,75 @@ -[ atomtypes ] -; name bond_type mass charge ptype sigma epsilon -Br BR 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -C C 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CA CA 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CB CB 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CC CC 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CK CK 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CM CM 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CN CN 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CQ CQ 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CR CR 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CT CT 0.0000 0.0000 A 3.39967e-01 4.57730e-01 -CV CV 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CW CW 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -C* C* 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -C0 Ca 0.0000 0.0000 A 3.05240e-01 1.92376e+00 -F F 0.0000 0.0000 A 3.11815e-01 2.55224e-01 -H H 0.0000 0.0000 A 1.06908e-01 6.56888e-02 -HC HC 0.0000 0.0000 A 2.64953e-01 6.56888e-02 -H1 H1 0.0000 0.0000 A 2.47135e-01 6.56888e-02 -H2 H2 0.0000 0.0000 A 2.29317e-01 6.56888e-02 -H3 H3 0.0000 0.0000 A 2.11499e-01 6.56888e-02 -HA HA 0.0000 0.0000 A 2.59964e-01 6.27600e-02 -H4 H4 0.0000 0.0000 A 2.51055e-01 6.27600e-02 -H5 H5 0.0000 0.0000 A 2.42146e-01 6.27600e-02 -HO HO 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -HS HS 0.0000 0.0000 A 1.06908e-01 6.56888e-02 -HW HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -HP HP 0.0000 0.0000 A 1.95998e-01 6.56888e-02 -I I 0.0000 0.0000 A 4.18722e-01 1.67360e+00 -Cl Cl 0.0000 0.0000 A 4.40104e-01 4.18400e-01 -Na Na 0.0000 0.0000 A 3.32840e-01 1.15897e-02 -IB IB 0.0000 0.0000 A 8.90899e-01 4.18400e-01 -MG Mg 0.0000 0.0000 A 1.41225e-01 3.74342e+00 -N N 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -NA NA 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -NB NB 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -NC NC 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -N2 N2 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -N3 N3 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -N* N* 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -O O 0.0000 0.0000 A 2.95992e-01 8.78640e-01 -OW OW 0.0000 0.0000 A 3.15061e-01 6.36386e-01 -OH OH 0.0000 0.0000 A 3.06647e-01 8.80314e-01 -OS OS 0.0000 0.0000 A 3.00001e-01 7.11280e-01 -O2 O2 0.0000 0.0000 A 2.95992e-01 8.78640e-01 -P P 0.0000 0.0000 A 3.74177e-01 8.36800e-01 -S S 0.0000 0.0000 A 3.56359e-01 1.04600e+00 -SH SH 0.0000 0.0000 A 3.56359e-01 1.04600e+00 -CU CU 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -FE FE 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -K K 0.0000 0.0000 A 4.73602e-01 1.37235e-03 -Rb Rb 0.0000 0.0000 A 5.26699e-01 7.11280e-04 -Cs Cs 0.0000 0.0000 A 6.04920e-01 3.37230e-04 -; spc water - use only with spc.itp & settles -OW_spc OW 0.0000 0.0000 A 3.16557e-01 6.50629e-01 -HW_spc HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -Li Li 0.0000 0.0000 A 2.02590e-01 7.65672e-02 -Zn Zn 0.0000 0.0000 A 1.95998e-01 5.23000e-02 -;tip4p-EW -HW_tip4pew HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -OW_tip4pew OW 0.0000 0.0000 A 3.16435e-01 6.80946e-01 -; tip4p -HW_tip4p HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -OW_tip4p OW 0.0000 0.0000 A 3.15365e-01 6.48520e-01 -;tip5p -HW_tip5p HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -OW_tip5p OW 0.0000 0.0000 A 3.12000e-01 6.69440e-01 -;tip3p heavy -HW_tip3p HW 4.0320 0.0000 A 0.00000e+00 0.00000e+00 -OW_tip3p OW 9.9520 0.0000 A 3.15061e-01 6.36386e-01 -; dummy defs -; MW=Dummy mass for tip4p/EW/5p water extra point charge -MW MW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -; Dummy masses for rigid CH3 and NH3 groups -MCH3 MCH3 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -MNH3 MNH3 0.0000 0.0000 A 0.00000e+00 0.00000e+00 +[ atomtypes ] +; name at.num mass charge ptype sigma epsilon +Br 35 79.90 0.0000 A 0.00000e+00 0.00000e+00 +C 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CA 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CB 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CC 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CK 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CM 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CN 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CQ 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CR 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CT 6 12.01 0.0000 A 3.39967e-01 4.57730e-01 +CV 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CW 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +C* 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +C0 20 40.08 0.0000 A 3.05240e-01 1.92376e+00 +F 9 19.00 0.0000 A 3.11815e-01 2.55224e-01 +H 1 1.008 0.0000 A 1.06908e-01 6.56888e-02 +HC 1 1.008 0.0000 A 2.64953e-01 6.56888e-02 +H1 1 1.008 0.0000 A 2.47135e-01 6.56888e-02 +H2 1 1.008 0.0000 A 2.29317e-01 6.56888e-02 +H3 1 1.008 0.0000 A 2.11499e-01 6.56888e-02 +HA 1 1.008 0.0000 A 2.59964e-01 6.27600e-02 +H4 1 1.008 0.0000 A 2.51055e-01 6.27600e-02 +H5 1 1.008 0.0000 A 2.42146e-01 6.27600e-02 +HO 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +HS 1 1.008 0.0000 A 1.06908e-01 6.56888e-02 +HW 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +HP 1 1.008 0.0000 A 1.95998e-01 6.56888e-02 +I 53 126.9 0.0000 A 4.18722e-01 1.67360e+00 +Cl 17 35.45 0.0000 A 4.40104e-01 4.18400e-01 +Na 11 22.99 0.0000 A 3.32840e-01 1.15897e-02 +IB 0 131.0 0.0000 A 8.90899e-01 4.18400e-01 +MG 12 24.305 0.0000 A 1.41225e-01 3.74342e+00 +N 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +NA 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +NB 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +NC 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +N2 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +N3 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +N* 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +O 8 16.00 0.0000 A 2.95992e-01 8.78640e-01 +OW 8 16.00 0.0000 A 3.15061e-01 6.36386e-01 +OH 8 16.00 0.0000 A 3.06647e-01 8.80314e-01 +OS 8 16.00 0.0000 A 3.00001e-01 7.11280e-01 +O2 8 16.00 0.0000 A 2.95992e-01 8.78640e-01 +P 15 30.97 0.0000 A 3.74177e-01 8.36800e-01 +S 16 32.06 0.0000 A 3.56359e-01 1.04600e+00 +SH 16 32.06 0.0000 A 3.56359e-01 1.04600e+00 +CU 29 63.55 0.0000 A 3.39967e-01 3.59824e-01 +FE 26 55.00 0.0000 A 0.00000e+00 0.00000e+00 +K 19 39.10 0.0000 A 4.73602e-01 1.37235e-03 +Rb 37 85.47 0.0000 A 5.26699e-01 7.11280e-04 +Cs 55 132.91 0.0000 A 6.04920e-01 3.37230e-04 +; spc water - use only with spc.itp & settles +OW_spc 8 15.9994 0.0000 A 3.16557e-01 6.50629e-01 +HW_spc 1 1.0080 0.0000 A 0.00000e+00 0.00000e+00 +Li 3 6.94 0.0000 A 2.02590e-01 7.65672e-02 +Zn 30 65.4 0.0000 A 1.95998e-01 5.23000e-02 +;tip4p-EW +HW_tip4pew 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +OW_tip4pew 8 16.00 0.0000 A 3.16435e-01 6.80946e-01 +; tip4p +HW_tip4p 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +OW_tip4p 8 16.00 0.0000 A 3.15365e-01 6.48520e-01 +;tip5p +HW_tip5p 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +OW_tip5p 8 16.00 0.0000 A 3.12000e-01 6.69440e-01 +; dummy defs +; MW=Dummy mass for tip4p/EW/5p water extra point charge +MW 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 +; Dummy masses for rigid CH3 and NH3 groups +MCH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 +MNH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 diff --git a/share/top/amber99sb.ff/atomtypes.atp b/share/top/amber99sb.ff/atomtypes.atp dissimilarity index 87% index 1edd14f6ae..a31392919a 100644 --- a/share/top/amber99sb.ff/atomtypes.atp +++ b/share/top/amber99sb.ff/atomtypes.atp @@ -1,68 +1,66 @@ -Br 79.90000 ; BR bromine -C 12.01000 ; C sp2 C carbonyl group -CA 12.01000 ; CA sp2 C pure aromatic (benzene) -CB 12.01000 ; CB sp2 aromatic C, 5&6 membered ring junction -CC 12.01000 ; CC sp2 aromatic C, 5 memb. ring HIS -CK 12.01000 ; CK sp2 C 5 memb.ring in purines -CM 12.01000 ; CM sp2 C pyrimidines in pos. 5 & 6 -CN 12.01000 ; CN sp2 C aromatic 5&6 memb.ring junct.(TRP) -CQ 12.01000 ; CQ sp2 C in 5 mem.ring of purines between 2 N -CR 12.01000 ; CR sp2 arom as CQ but in HIS -CT 12.01000 ; CT sp3 aliphatic C -CV 12.01000 ; CV sp2 arom. 5 memb.ring w/1 N and 1 H (HIS) -CW 12.01000 ; CW sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS) -C* 12.01000 ; C* sp2 arom. 5 memb.ring w/1 subst. (TRP) -C0 40.08000 ; Ca2+ calcium -F 19.00000 ; F fluorine -H 1.00800 ; H H bonded to nitrogen atoms -HC 1.00800 ; HC H aliph. bond. to C without electrwd.group -H1 1.00800 ; H1 H aliph. bond. to C with 1 electrwd. group -H2 1.00800 ; H2 H aliph. bond. to C with 2 electrwd.groups -H3 1.00800 ; H3 H aliph. bond. to C with 3 eletrwd.groups -HA 1.00800 ; HA H arom. bond. to C without elctrwd. groups -H4 1.00800 ; H4 H arom. bond. to C with 1 electrwd. group -H5 1.00800 ; H5 H arom. bond. to C with 2 electrwd. groups -HO 1.00800 ; HO hydroxyl group -HS 1.00800 ; HS hydrogen bonded to sulphur -HW 1.00800 ; HW H in TIP3P water -HP 1.00800 ; HP H bonded to C next to positively charged gr -I 126.90000 ; I iodine -Cl 35.45000 ; Cl- -Na 22.99000 ; Na+ -IB 131.00000 ; IB 'big ion w/ waters' for vacuum (Na+, 6H2O) -MG 24.30000 ; Mg2+ magnesium -N 14.01000 ; N sp2 nitrogen in amide groups -NA 14.01000 ; NA sp2 N in 5 memb.ring w/H atom (HIS) -NB 14.01000 ; NB sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) -NC 14.01000 ; NC sp2 N in 6 memb.ring w/LP (ADE,GUA) -N2 14.01000 ; N2 sp2 N in amino groups -N3 14.01000 ; N3 sp3 N for charged amino groups (Lys, etc) -N* 14.01000 ; N* sp2 N -O 16.00000 ; O carbonyl group oxygen -OW 16.00000 ; OW oxygen in TIP3P water -OH 16.00000 ; OH oxygen in hydroxyl group -OS 16.00000 ; OS ether and ester oxygen -O2 16.00000 ; O2 carboxyl and phosphate group oxygen -P 30.97000 ; P phosphate -S 32.06000 ; S sulphur in disulfide linkage -SH 32.06000 ; SH sulphur in cystine -CU 63.55000 ; CU copper -FE 55.00000 ; FE iron -K 39.10000 ; K+ potassium -Rb 85.47000 ; Rb+ rubidium -Cs 132.90000 ; Cs+ cesium -OW_spc 15.99940 ; SPC Water OW -HW_spc 1.00800 ; SPC Water HW -Li 6.94000 ; Li+ from parm94/96 -Zn 65.40000 ; Zn2+ from parm99 -HW_tip4pew 1.00800 ; tip4pEW HW -OW_tip4pew 16.00000 ; tip4pEW OW -HW_tip4p 1.00800 ; tip4p HW -OW_tip4p 16.00000 ; tip4p OW -HW_tip5p 1.00800 ; tip5p HW -OW_tip5p 16.00000 ; tip5p OW -HW_tip3p 4.03200 ; TIP3P HEAVY dummy water HW -OW_tip3p 9.95200 ; TIP3P heavy dummy water OW -MW 0.00000 ; Dummy mass for tip4p/5p water extra point charge -MCH3 0.00000 ; Dummy mass in rigid tetrahedral CH3 group -MNH3 0.00000 ; Dummy mass in rigid tetrahedral NH3 group +Br 79.90000 ; bromine +C 12.01000 ; sp2 C carbonyl group +CA 12.01000 ; sp2 C pure aromatic (benzene) +CB 12.01000 ; sp2 aromatic C, 5&6 membered ring junction +CC 12.01000 ; sp2 aromatic C, 5 memb. ring HIS +CK 12.01000 ; sp2 C 5 memb.ring in purines +CM 12.01000 ; sp2 C pyrimidines in pos. 5 & 6 +CN 12.01000 ; sp2 C aromatic 5&6 memb.ring junct.(TRP) +CQ 12.01000 ; sp2 C in 5 mem.ring of purines between 2 N +CR 12.01000 ; sp2 arom as CQ but in HIS +CT 12.01000 ; sp3 aliphatic C +CV 12.01000 ; sp2 arom. 5 memb.ring w/1 N and 1 H (HIS) +CW 12.01000 ; sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS) +C* 12.01000 ; sp2 arom. 5 memb.ring w/1 subst. (TRP) +C0 40.08000 ; calcium +F 19.00000 ; fluorine +H 1.00800 ; H bonded to nitrogen atoms +HC 1.00800 ; H aliph. bond. to C without electrwd.group +H1 1.00800 ; H aliph. bond. to C with 1 electrwd. group +H2 1.00800 ; H aliph. bond. to C with 2 electrwd.groups +H3 1.00800 ; H aliph. bond. to C with 3 eletrwd.groups +HA 1.00800 ; H arom. bond. to C without elctrwd. groups +H4 1.00800 ; H arom. bond. to C with 1 electrwd. group +H5 1.00800 ; H arom. bond. to C with 2 electrwd. groups +HO 1.00800 ; hydroxyl group +HS 1.00800 ; hydrogen bonded to sulphur (pol?) +HW 1.00800 ; H in TIP3P water +HP 1.00800 ; H bonded to C next to positively charged gr +I 126.90000 ; iodine (Applequist) +Cl 35.45000 ; chlorine (Applequist) +Na 22.99000 ; Na+, ions pol:J.PhysC,11,1541,(1978) +IB 131.00000 ; 'big ion w/ waters' for vacuum (Na+, 6H2O) +MG 24.30500 ; magnesium +N 14.01000 ; sp2 nitrogen in amide groups +NA 14.01000 ; sp2 N in 5 memb.ring w/H atom (HIS) +NB 14.01000 ; sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) +NC 14.01000 ; sp2 N in 6 memb.ring w/LP (ADE,GUA) +N2 14.01000 ; sp2 N in amino groups +N3 14.01000 ; sp3 N for charged amino groups (Lys, etc) +N* 14.01000 ; sp2 N +O 16.00000 ; carbonyl group oxygen +OW 16.00000 ; oxygen in TIP3P water +OH 16.00000 ; oxygen in hydroxyl group +OS 16.00000 ; ether and ester oxygen +O2 16.00000 ; carboxyl and phosphate group oxygen +P 30.97000 ; phosphate,pol:JACS,112,8543,90,K.J.Miller +S 32.06000 ; S in disulfide linkage,pol:JPC,102,2399,98 +SH 32.06000 ; S in cystine +CU 63.55000 ; copper +FE 55.00000 ; iron +K 39.10000 ; potassium +Rb 85.47000 ; rubidium +Cs 132.90000 ; cesium +OW_spc 15.99940 ; SPC Water OW +HW_spc 1.00800 ; SPC Water HW +Li 6.94000 ; lithium, ions pol:J.PhysC,11,1541,(1978) +Zn 65.40000 ; Zn2+ +HW_tip4pew 1.00800 ; tip4pEW HW +OW_tip4pew 16.00000 ; tip4pEW OW +HW_tip4p 1.00800 ; tip4p HW +OW_tip4p 16.00000 ; tip4p OW +HW_tip5p 1.00800 ; tip5p HW +OW_tip5p 16.00000 ; tip5p OW +MW 0.00000 ; Virtual site for tip4p/5p water point charge +MCH3 0.00000 ; Dummy mass in rigid tetrahedral CH3 group +MNH3 0.00000 ; Dummy mass in rigid tetrahedral NH3 group diff --git a/share/top/amber99sb.ff/ffnonbonded.itp b/share/top/amber99sb.ff/ffnonbonded.itp dissimilarity index 93% index 7dd6009240..ef3fde6d98 100644 --- a/share/top/amber99sb.ff/ffnonbonded.itp +++ b/share/top/amber99sb.ff/ffnonbonded.itp @@ -1,78 +1,75 @@ -[ atomtypes ] -; name bond_type mass charge ptype sigma epsilon -Br BR 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -C C 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CA CA 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CB CB 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CC CC 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CK CK 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CM CM 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CN CN 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CQ CQ 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CR CR 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CT CT 0.0000 0.0000 A 3.39967e-01 4.57730e-01 -CV CV 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CW CW 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -C* C* 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -C0 Ca 0.0000 0.0000 A 3.05240e-01 1.92376e+00 -F F 0.0000 0.0000 A 3.11815e-01 2.55224e-01 -H H 0.0000 0.0000 A 1.06908e-01 6.56888e-02 -HC HC 0.0000 0.0000 A 2.64953e-01 6.56888e-02 -H1 H1 0.0000 0.0000 A 2.47135e-01 6.56888e-02 -H2 H2 0.0000 0.0000 A 2.29317e-01 6.56888e-02 -H3 H3 0.0000 0.0000 A 2.11499e-01 6.56888e-02 -HA HA 0.0000 0.0000 A 2.59964e-01 6.27600e-02 -H4 H4 0.0000 0.0000 A 2.51055e-01 6.27600e-02 -H5 H5 0.0000 0.0000 A 2.42146e-01 6.27600e-02 -HO HO 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -HS HS 0.0000 0.0000 A 1.06908e-01 6.56888e-02 -HW HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -HP HP 0.0000 0.0000 A 1.95998e-01 6.56888e-02 -I I 0.0000 0.0000 A 4.18722e-01 1.67360e+00 -Cl Cl 0.0000 0.0000 A 4.40104e-01 4.18400e-01 -Na Na 0.0000 0.0000 A 3.32840e-01 1.15897e-02 -IB IB 0.0000 0.0000 A 8.90899e-01 4.18400e-01 -MG Mg 0.0000 0.0000 A 1.41225e-01 3.74342e+00 -N N 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -NA NA 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -NB NB 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -NC NC 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -N2 N2 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -N3 N3 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -N* N* 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -O O 0.0000 0.0000 A 2.95992e-01 8.78640e-01 -OW OW 0.0000 0.0000 A 3.15061e-01 6.36386e-01 -OH OH 0.0000 0.0000 A 3.06647e-01 8.80314e-01 -OS OS 0.0000 0.0000 A 3.00001e-01 7.11280e-01 -O2 O2 0.0000 0.0000 A 2.95992e-01 8.78640e-01 -P P 0.0000 0.0000 A 3.74177e-01 8.36800e-01 -S S 0.0000 0.0000 A 3.56359e-01 1.04600e+00 -SH SH 0.0000 0.0000 A 3.56359e-01 1.04600e+00 -CU CU 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -FE FE 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -K K 0.0000 0.0000 A 4.73602e-01 1.37235e-03 -Rb Rb 0.0000 0.0000 A 5.26699e-01 7.11280e-04 -Cs Cs 0.0000 0.0000 A 6.04920e-01 3.37230e-04 -; spc water - use only with spc.itp & settles -OW_spc OW 0.0000 0.0000 A 3.16557e-01 6.50629e-01 -HW_spc HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -Li Li 0.0000 0.0000 A 2.02590e-01 7.65672e-02 -Zn Zn 0.0000 0.0000 A 1.95998e-01 5.23000e-02 -;tip4p-EW -HW_tip4pew HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -OW_tip4pew OW 0.0000 0.0000 A 3.16435e-01 6.80946e-01 -; tip4p -HW_tip4p HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -OW_tip4p OW 0.0000 0.0000 A 3.15365e-01 6.48520e-01 -;tip5p -HW_tip5p HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -OW_tip5p OW 0.0000 0.0000 A 3.12000e-01 6.69440e-01 -;tip3p heavy -HW_tip3p HW 4.0320 0.0000 A 0.00000e+00 0.00000e+00 -OW_tip3p OW 9.9520 0.0000 A 3.15061e-01 6.36386e-01 -; dummy defs -; MW=Dummy mass for tip4p/EW/5p water extra point charge -MW MW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -; Dummy masses for rigid CH3 and NH3 groups -MCH3 MCH3 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -MNH3 MNH3 0.0000 0.0000 A 0.00000e+00 0.00000e+00 +[ atomtypes ] +; name at.num mass charge ptype sigma epsilon +Br 35 79.90 0.0000 A 0.00000e+00 0.00000e+00 +C 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CA 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CB 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CC 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CK 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CM 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CN 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CQ 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CR 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CT 6 12.01 0.0000 A 3.39967e-01 4.57730e-01 +CV 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CW 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +C* 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +C0 20 40.08 0.0000 A 3.05240e-01 1.92376e+00 +F 9 19.00 0.0000 A 3.11815e-01 2.55224e-01 +H 1 1.008 0.0000 A 1.06908e-01 6.56888e-02 +HC 1 1.008 0.0000 A 2.64953e-01 6.56888e-02 +H1 1 1.008 0.0000 A 2.47135e-01 6.56888e-02 +H2 1 1.008 0.0000 A 2.29317e-01 6.56888e-02 +H3 1 1.008 0.0000 A 2.11499e-01 6.56888e-02 +HA 1 1.008 0.0000 A 2.59964e-01 6.27600e-02 +H4 1 1.008 0.0000 A 2.51055e-01 6.27600e-02 +H5 1 1.008 0.0000 A 2.42146e-01 6.27600e-02 +HO 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +HS 1 1.008 0.0000 A 1.06908e-01 6.56888e-02 +HW 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +HP 1 1.008 0.0000 A 1.95998e-01 6.56888e-02 +I 53 126.9 0.0000 A 4.18722e-01 1.67360e+00 +Cl 17 35.45 0.0000 A 4.40104e-01 4.18400e-01 +Na 11 22.99 0.0000 A 3.32840e-01 1.15897e-02 +IB 0 131.0 0.0000 A 8.90899e-01 4.18400e-01 +MG 12 24.305 0.0000 A 1.41225e-01 3.74342e+00 +N 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +NA 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +NB 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +NC 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +N2 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +N3 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +N* 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +O 8 16.00 0.0000 A 2.95992e-01 8.78640e-01 +OW 8 16.00 0.0000 A 3.15061e-01 6.36386e-01 +OH 8 16.00 0.0000 A 3.06647e-01 8.80314e-01 +OS 8 16.00 0.0000 A 3.00001e-01 7.11280e-01 +O2 8 16.00 0.0000 A 2.95992e-01 8.78640e-01 +P 15 30.97 0.0000 A 3.74177e-01 8.36800e-01 +S 16 32.06 0.0000 A 3.56359e-01 1.04600e+00 +SH 16 32.06 0.0000 A 3.56359e-01 1.04600e+00 +CU 29 63.55 0.0000 A 3.39967e-01 3.59824e-01 +FE 26 55.00 0.0000 A 0.00000e+00 0.00000e+00 +K 19 39.10 0.0000 A 4.73602e-01 1.37235e-03 +Rb 37 85.47 0.0000 A 5.26699e-01 7.11280e-04 +Cs 55 132.91 0.0000 A 6.04920e-01 3.37230e-04 +; spc water - use only with spc.itp & settles +OW_spc 8 15.9994 0.0000 A 3.16557e-01 6.50629e-01 +HW_spc 1 1.0080 0.0000 A 0.00000e+00 0.00000e+00 +Li 3 6.94 0.0000 A 2.02590e-01 7.65672e-02 +Zn 30 65.4 0.0000 A 1.95998e-01 5.23000e-02 +;tip4p-EW +HW_tip4pew 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +OW_tip4pew 8 16.00 0.0000 A 3.16435e-01 6.80946e-01 +; tip4p +HW_tip4p 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +OW_tip4p 8 16.00 0.0000 A 3.15365e-01 6.48520e-01 +;tip5p +HW_tip5p 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +OW_tip5p 8 16.00 0.0000 A 3.12000e-01 6.69440e-01 +; dummy defs +; MW=Dummy mass for tip4p/EW/5p water extra point charge +MW 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 +; Dummy masses for rigid CH3 and NH3 groups +MCH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 +MNH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 diff --git a/share/top/amberGS.ff/atomtypes.atp b/share/top/amberGS.ff/atomtypes.atp dissimilarity index 87% index 1edd14f6ae..a31392919a 100644 --- a/share/top/amberGS.ff/atomtypes.atp +++ b/share/top/amberGS.ff/atomtypes.atp @@ -1,68 +1,66 @@ -Br 79.90000 ; BR bromine -C 12.01000 ; C sp2 C carbonyl group -CA 12.01000 ; CA sp2 C pure aromatic (benzene) -CB 12.01000 ; CB sp2 aromatic C, 5&6 membered ring junction -CC 12.01000 ; CC sp2 aromatic C, 5 memb. ring HIS -CK 12.01000 ; CK sp2 C 5 memb.ring in purines -CM 12.01000 ; CM sp2 C pyrimidines in pos. 5 & 6 -CN 12.01000 ; CN sp2 C aromatic 5&6 memb.ring junct.(TRP) -CQ 12.01000 ; CQ sp2 C in 5 mem.ring of purines between 2 N -CR 12.01000 ; CR sp2 arom as CQ but in HIS -CT 12.01000 ; CT sp3 aliphatic C -CV 12.01000 ; CV sp2 arom. 5 memb.ring w/1 N and 1 H (HIS) -CW 12.01000 ; CW sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS) -C* 12.01000 ; C* sp2 arom. 5 memb.ring w/1 subst. (TRP) -C0 40.08000 ; Ca2+ calcium -F 19.00000 ; F fluorine -H 1.00800 ; H H bonded to nitrogen atoms -HC 1.00800 ; HC H aliph. bond. to C without electrwd.group -H1 1.00800 ; H1 H aliph. bond. to C with 1 electrwd. group -H2 1.00800 ; H2 H aliph. bond. to C with 2 electrwd.groups -H3 1.00800 ; H3 H aliph. bond. to C with 3 eletrwd.groups -HA 1.00800 ; HA H arom. bond. to C without elctrwd. groups -H4 1.00800 ; H4 H arom. bond. to C with 1 electrwd. group -H5 1.00800 ; H5 H arom. bond. to C with 2 electrwd. groups -HO 1.00800 ; HO hydroxyl group -HS 1.00800 ; HS hydrogen bonded to sulphur -HW 1.00800 ; HW H in TIP3P water -HP 1.00800 ; HP H bonded to C next to positively charged gr -I 126.90000 ; I iodine -Cl 35.45000 ; Cl- -Na 22.99000 ; Na+ -IB 131.00000 ; IB 'big ion w/ waters' for vacuum (Na+, 6H2O) -MG 24.30000 ; Mg2+ magnesium -N 14.01000 ; N sp2 nitrogen in amide groups -NA 14.01000 ; NA sp2 N in 5 memb.ring w/H atom (HIS) -NB 14.01000 ; NB sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) -NC 14.01000 ; NC sp2 N in 6 memb.ring w/LP (ADE,GUA) -N2 14.01000 ; N2 sp2 N in amino groups -N3 14.01000 ; N3 sp3 N for charged amino groups (Lys, etc) -N* 14.01000 ; N* sp2 N -O 16.00000 ; O carbonyl group oxygen -OW 16.00000 ; OW oxygen in TIP3P water -OH 16.00000 ; OH oxygen in hydroxyl group -OS 16.00000 ; OS ether and ester oxygen -O2 16.00000 ; O2 carboxyl and phosphate group oxygen -P 30.97000 ; P phosphate -S 32.06000 ; S sulphur in disulfide linkage -SH 32.06000 ; SH sulphur in cystine -CU 63.55000 ; CU copper -FE 55.00000 ; FE iron -K 39.10000 ; K+ potassium -Rb 85.47000 ; Rb+ rubidium -Cs 132.90000 ; Cs+ cesium -OW_spc 15.99940 ; SPC Water OW -HW_spc 1.00800 ; SPC Water HW -Li 6.94000 ; Li+ from parm94/96 -Zn 65.40000 ; Zn2+ from parm99 -HW_tip4pew 1.00800 ; tip4pEW HW -OW_tip4pew 16.00000 ; tip4pEW OW -HW_tip4p 1.00800 ; tip4p HW -OW_tip4p 16.00000 ; tip4p OW -HW_tip5p 1.00800 ; tip5p HW -OW_tip5p 16.00000 ; tip5p OW -HW_tip3p 4.03200 ; TIP3P HEAVY dummy water HW -OW_tip3p 9.95200 ; TIP3P heavy dummy water OW -MW 0.00000 ; Dummy mass for tip4p/5p water extra point charge -MCH3 0.00000 ; Dummy mass in rigid tetrahedral CH3 group -MNH3 0.00000 ; Dummy mass in rigid tetrahedral NH3 group +Br 79.90000 ; bromine +C 12.01000 ; sp2 C carbonyl group +CA 12.01000 ; sp2 C pure aromatic (benzene) +CB 12.01000 ; sp2 aromatic C, 5&6 membered ring junction +CC 12.01000 ; sp2 aromatic C, 5 memb. ring HIS +CK 12.01000 ; sp2 C 5 memb.ring in purines +CM 12.01000 ; sp2 C pyrimidines in pos. 5 & 6 +CN 12.01000 ; sp2 C aromatic 5&6 memb.ring junct.(TRP) +CQ 12.01000 ; sp2 C in 5 mem.ring of purines between 2 N +CR 12.01000 ; sp2 arom as CQ but in HIS +CT 12.01000 ; sp3 aliphatic C +CV 12.01000 ; sp2 arom. 5 memb.ring w/1 N and 1 H (HIS) +CW 12.01000 ; sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS) +C* 12.01000 ; sp2 arom. 5 memb.ring w/1 subst. (TRP) +C0 40.08000 ; calcium +F 19.00000 ; fluorine +H 1.00800 ; H bonded to nitrogen atoms +HC 1.00800 ; H aliph. bond. to C without electrwd.group +H1 1.00800 ; H aliph. bond. to C with 1 electrwd. group +H2 1.00800 ; H aliph. bond. to C with 2 electrwd.groups +H3 1.00800 ; H aliph. bond. to C with 3 eletrwd.groups +HA 1.00800 ; H arom. bond. to C without elctrwd. groups +H4 1.00800 ; H arom. bond. to C with 1 electrwd. group +H5 1.00800 ; H arom. bond. to C with 2 electrwd. groups +HO 1.00800 ; hydroxyl group +HS 1.00800 ; hydrogen bonded to sulphur (pol?) +HW 1.00800 ; H in TIP3P water +HP 1.00800 ; H bonded to C next to positively charged gr +I 126.90000 ; iodine (Applequist) +Cl 35.45000 ; chlorine (Applequist) +Na 22.99000 ; Na+, ions pol:J.PhysC,11,1541,(1978) +IB 131.00000 ; 'big ion w/ waters' for vacuum (Na+, 6H2O) +MG 24.30500 ; magnesium +N 14.01000 ; sp2 nitrogen in amide groups +NA 14.01000 ; sp2 N in 5 memb.ring w/H atom (HIS) +NB 14.01000 ; sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) +NC 14.01000 ; sp2 N in 6 memb.ring w/LP (ADE,GUA) +N2 14.01000 ; sp2 N in amino groups +N3 14.01000 ; sp3 N for charged amino groups (Lys, etc) +N* 14.01000 ; sp2 N +O 16.00000 ; carbonyl group oxygen +OW 16.00000 ; oxygen in TIP3P water +OH 16.00000 ; oxygen in hydroxyl group +OS 16.00000 ; ether and ester oxygen +O2 16.00000 ; carboxyl and phosphate group oxygen +P 30.97000 ; phosphate,pol:JACS,112,8543,90,K.J.Miller +S 32.06000 ; S in disulfide linkage,pol:JPC,102,2399,98 +SH 32.06000 ; S in cystine +CU 63.55000 ; copper +FE 55.00000 ; iron +K 39.10000 ; potassium +Rb 85.47000 ; rubidium +Cs 132.90000 ; cesium +OW_spc 15.99940 ; SPC Water OW +HW_spc 1.00800 ; SPC Water HW +Li 6.94000 ; lithium, ions pol:J.PhysC,11,1541,(1978) +Zn 65.40000 ; Zn2+ +HW_tip4pew 1.00800 ; tip4pEW HW +OW_tip4pew 16.00000 ; tip4pEW OW +HW_tip4p 1.00800 ; tip4p HW +OW_tip4p 16.00000 ; tip4p OW +HW_tip5p 1.00800 ; tip5p HW +OW_tip5p 16.00000 ; tip5p OW +MW 0.00000 ; Virtual site for tip4p/5p water point charge +MCH3 0.00000 ; Dummy mass in rigid tetrahedral CH3 group +MNH3 0.00000 ; Dummy mass in rigid tetrahedral NH3 group diff --git a/share/top/amberGS.ff/ffnonbonded.itp b/share/top/amberGS.ff/ffnonbonded.itp dissimilarity index 93% index 7dd6009240..ef3fde6d98 100644 --- a/share/top/amberGS.ff/ffnonbonded.itp +++ b/share/top/amberGS.ff/ffnonbonded.itp @@ -1,78 +1,75 @@ -[ atomtypes ] -; name bond_type mass charge ptype sigma epsilon -Br BR 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -C C 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CA CA 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CB CB 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CC CC 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CK CK 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CM CM 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CN CN 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CQ CQ 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CR CR 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CT CT 0.0000 0.0000 A 3.39967e-01 4.57730e-01 -CV CV 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -CW CW 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -C* C* 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -C0 Ca 0.0000 0.0000 A 3.05240e-01 1.92376e+00 -F F 0.0000 0.0000 A 3.11815e-01 2.55224e-01 -H H 0.0000 0.0000 A 1.06908e-01 6.56888e-02 -HC HC 0.0000 0.0000 A 2.64953e-01 6.56888e-02 -H1 H1 0.0000 0.0000 A 2.47135e-01 6.56888e-02 -H2 H2 0.0000 0.0000 A 2.29317e-01 6.56888e-02 -H3 H3 0.0000 0.0000 A 2.11499e-01 6.56888e-02 -HA HA 0.0000 0.0000 A 2.59964e-01 6.27600e-02 -H4 H4 0.0000 0.0000 A 2.51055e-01 6.27600e-02 -H5 H5 0.0000 0.0000 A 2.42146e-01 6.27600e-02 -HO HO 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -HS HS 0.0000 0.0000 A 1.06908e-01 6.56888e-02 -HW HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -HP HP 0.0000 0.0000 A 1.95998e-01 6.56888e-02 -I I 0.0000 0.0000 A 4.18722e-01 1.67360e+00 -Cl Cl 0.0000 0.0000 A 4.40104e-01 4.18400e-01 -Na Na 0.0000 0.0000 A 3.32840e-01 1.15897e-02 -IB IB 0.0000 0.0000 A 8.90899e-01 4.18400e-01 -MG Mg 0.0000 0.0000 A 1.41225e-01 3.74342e+00 -N N 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -NA NA 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -NB NB 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -NC NC 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -N2 N2 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -N3 N3 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -N* N* 0.0000 0.0000 A 3.25000e-01 7.11280e-01 -O O 0.0000 0.0000 A 2.95992e-01 8.78640e-01 -OW OW 0.0000 0.0000 A 3.15061e-01 6.36386e-01 -OH OH 0.0000 0.0000 A 3.06647e-01 8.80314e-01 -OS OS 0.0000 0.0000 A 3.00001e-01 7.11280e-01 -O2 O2 0.0000 0.0000 A 2.95992e-01 8.78640e-01 -P P 0.0000 0.0000 A 3.74177e-01 8.36800e-01 -S S 0.0000 0.0000 A 3.56359e-01 1.04600e+00 -SH SH 0.0000 0.0000 A 3.56359e-01 1.04600e+00 -CU CU 0.0000 0.0000 A 3.39967e-01 3.59824e-01 -FE FE 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -K K 0.0000 0.0000 A 4.73602e-01 1.37235e-03 -Rb Rb 0.0000 0.0000 A 5.26699e-01 7.11280e-04 -Cs Cs 0.0000 0.0000 A 6.04920e-01 3.37230e-04 -; spc water - use only with spc.itp & settles -OW_spc OW 0.0000 0.0000 A 3.16557e-01 6.50629e-01 -HW_spc HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -Li Li 0.0000 0.0000 A 2.02590e-01 7.65672e-02 -Zn Zn 0.0000 0.0000 A 1.95998e-01 5.23000e-02 -;tip4p-EW -HW_tip4pew HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -OW_tip4pew OW 0.0000 0.0000 A 3.16435e-01 6.80946e-01 -; tip4p -HW_tip4p HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -OW_tip4p OW 0.0000 0.0000 A 3.15365e-01 6.48520e-01 -;tip5p -HW_tip5p HW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -OW_tip5p OW 0.0000 0.0000 A 3.12000e-01 6.69440e-01 -;tip3p heavy -HW_tip3p HW 4.0320 0.0000 A 0.00000e+00 0.00000e+00 -OW_tip3p OW 9.9520 0.0000 A 3.15061e-01 6.36386e-01 -; dummy defs -; MW=Dummy mass for tip4p/EW/5p water extra point charge -MW MW 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -; Dummy masses for rigid CH3 and NH3 groups -MCH3 MCH3 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -MNH3 MNH3 0.0000 0.0000 A 0.00000e+00 0.00000e+00 +[ atomtypes ] +; name at.num mass charge ptype sigma epsilon +Br 35 79.90 0.0000 A 0.00000e+00 0.00000e+00 +C 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CA 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CB 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CC 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CK 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CM 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CN 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CQ 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CR 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CT 6 12.01 0.0000 A 3.39967e-01 4.57730e-01 +CV 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +CW 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +C* 6 12.01 0.0000 A 3.39967e-01 3.59824e-01 +C0 20 40.08 0.0000 A 3.05240e-01 1.92376e+00 +F 9 19.00 0.0000 A 3.11815e-01 2.55224e-01 +H 1 1.008 0.0000 A 1.06908e-01 6.56888e-02 +HC 1 1.008 0.0000 A 2.64953e-01 6.56888e-02 +H1 1 1.008 0.0000 A 2.47135e-01 6.56888e-02 +H2 1 1.008 0.0000 A 2.29317e-01 6.56888e-02 +H3 1 1.008 0.0000 A 2.11499e-01 6.56888e-02 +HA 1 1.008 0.0000 A 2.59964e-01 6.27600e-02 +H4 1 1.008 0.0000 A 2.51055e-01 6.27600e-02 +H5 1 1.008 0.0000 A 2.42146e-01 6.27600e-02 +HO 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +HS 1 1.008 0.0000 A 1.06908e-01 6.56888e-02 +HW 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +HP 1 1.008 0.0000 A 1.95998e-01 6.56888e-02 +I 53 126.9 0.0000 A 4.18722e-01 1.67360e+00 +Cl 17 35.45 0.0000 A 4.40104e-01 4.18400e-01 +Na 11 22.99 0.0000 A 3.32840e-01 1.15897e-02 +IB 0 131.0 0.0000 A 8.90899e-01 4.18400e-01 +MG 12 24.305 0.0000 A 1.41225e-01 3.74342e+00 +N 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +NA 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +NB 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +NC 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +N2 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +N3 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +N* 7 14.01 0.0000 A 3.25000e-01 7.11280e-01 +O 8 16.00 0.0000 A 2.95992e-01 8.78640e-01 +OW 8 16.00 0.0000 A 3.15061e-01 6.36386e-01 +OH 8 16.00 0.0000 A 3.06647e-01 8.80314e-01 +OS 8 16.00 0.0000 A 3.00001e-01 7.11280e-01 +O2 8 16.00 0.0000 A 2.95992e-01 8.78640e-01 +P 15 30.97 0.0000 A 3.74177e-01 8.36800e-01 +S 16 32.06 0.0000 A 3.56359e-01 1.04600e+00 +SH 16 32.06 0.0000 A 3.56359e-01 1.04600e+00 +CU 29 63.55 0.0000 A 3.39967e-01 3.59824e-01 +FE 26 55.00 0.0000 A 0.00000e+00 0.00000e+00 +K 19 39.10 0.0000 A 4.73602e-01 1.37235e-03 +Rb 37 85.47 0.0000 A 5.26699e-01 7.11280e-04 +Cs 55 132.91 0.0000 A 6.04920e-01 3.37230e-04 +; spc water - use only with spc.itp & settles +OW_spc 8 15.9994 0.0000 A 3.16557e-01 6.50629e-01 +HW_spc 1 1.0080 0.0000 A 0.00000e+00 0.00000e+00 +Li 3 6.94 0.0000 A 2.02590e-01 7.65672e-02 +Zn 30 65.4 0.0000 A 1.95998e-01 5.23000e-02 +;tip4p-EW +HW_tip4pew 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +OW_tip4pew 8 16.00 0.0000 A 3.16435e-01 6.80946e-01 +; tip4p +HW_tip4p 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +OW_tip4p 8 16.00 0.0000 A 3.15365e-01 6.48520e-01 +;tip5p +HW_tip5p 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 +OW_tip5p 8 16.00 0.0000 A 3.12000e-01 6.69440e-01 +; dummy defs +; MW=Dummy mass for tip4p/EW/5p water extra point charge +MW 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 +; Dummy masses for rigid CH3 and NH3 groups +MCH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 +MNH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00 -- 2.11.4.GIT