From 5061e103a14c075183d48f6334daa346ffc6b1c7 Mon Sep 17 00:00:00 2001 From: Berk Hess Date: Mon, 26 Jul 2010 18:47:55 +0200 Subject: [PATCH] renamed amber LYP to LYS and changed names for water models in the rtp files --- share/top/amber03.ff/aminoacids.arn | 6 +-- share/top/amber03.ff/aminoacids.hdb | 6 +-- share/top/amber03.ff/aminoacids.r2b | 2 +- share/top/amber03.ff/aminoacids.rtp | 6 +-- share/top/amber94.ff/aminoacids.arn | 6 +-- share/top/amber94.ff/aminoacids.hdb | 6 +-- share/top/amber94.ff/aminoacids.r2b | 2 +- share/top/amber94.ff/aminoacids.rtp | 64 +++++--------------------- share/top/amber96.ff/aminoacids.arn | 6 +-- share/top/amber96.ff/aminoacids.hdb | 6 +-- share/top/amber96.ff/aminoacids.r2b | 2 +- share/top/amber96.ff/aminoacids.rtp | 64 +++++--------------------- share/top/amber99.ff/aminoacids.arn | 6 +-- share/top/amber99.ff/aminoacids.hdb | 6 +-- share/top/amber99.ff/aminoacids.r2b | 2 +- share/top/amber99.ff/aminoacids.rtp | 72 ++++++----------------------- share/top/amber99sb-ildn.ff/aminoacids.arn | 6 +-- share/top/amber99sb-ildn.ff/aminoacids.hdb | 6 +-- share/top/amber99sb-ildn.ff/aminoacids.r2b | 2 +- share/top/amber99sb-ildn.ff/aminoacids.rtp | 73 ++++++------------------------ share/top/amber99sb.ff/aminoacids.arn | 6 +-- share/top/amber99sb.ff/aminoacids.hdb | 6 +-- share/top/amber99sb.ff/aminoacids.r2b | 2 +- share/top/amber99sb.ff/aminoacids.rtp | 72 ++++++----------------------- share/top/amberGS.ff/aminoacids.arn | 6 +-- share/top/amberGS.ff/aminoacids.hdb | 6 +-- share/top/amberGS.ff/aminoacids.r2b | 2 +- share/top/amberGS.ff/aminoacids.rtp | 70 ++++++---------------------- 28 files changed, 133 insertions(+), 386 deletions(-) diff --git a/share/top/amber03.ff/aminoacids.arn b/share/top/amber03.ff/aminoacids.arn index 333fa567e6..253f8ba6f2 100644 --- a/share/top/amber03.ff/aminoacids.arn +++ b/share/top/amber03.ff/aminoacids.arn @@ -18,7 +18,7 @@ NTYR H H1 NGLU H H1 NASP H H1 - NLYP H H1 + NLYS H H1 NPRO H H1 NCYN H H1 NCYX H H1 @@ -65,8 +65,8 @@ CGLU OXT OC1 CASP O OC2 CASP OXT OC1 - CLYP O OC2 - CLYP OXT OC1 + CLYS O OC2 + CLYS OXT OC1 CPRO O OC2 CPRO OXT OC1 CCYN O OC2 diff --git a/share/top/amber03.ff/aminoacids.hdb b/share/top/amber03.ff/aminoacids.hdb index 6975ca41e6..90cb8582e8 100644 --- a/share/top/amber03.ff/aminoacids.hdb +++ b/share/top/amber03.ff/aminoacids.hdb @@ -128,7 +128,7 @@ ASP 3 1 1 H N -C CA 1 5 HA CA N CB C 2 6 HB CB CA CG -LYP 7 +LYS 7 1 1 H N -C CA 1 5 HA CA N CB C 2 6 HB CB CA CG @@ -337,7 +337,7 @@ CASP 4 1 5 HA CA N CB C 2 6 HB CB CA CG 1 1 OC1 C CA OC2 -CLYP 8 +CLYS 8 1 1 H N -C CA 1 5 HA CA N CB C 2 6 HB CB CA CG @@ -487,7 +487,7 @@ NASP 3 3 4 H N CA CB 1 5 HA CA N CB C 2 6 HB CB CA CG -NLYP 7 +NLYS 7 3 4 H N CA CB 1 5 HA CA N CB C 2 6 HB CB CA CG diff --git a/share/top/amber03.ff/aminoacids.r2b b/share/top/amber03.ff/aminoacids.r2b index 48422d81dc..22ac11c6e4 100644 --- a/share/top/amber03.ff/aminoacids.r2b +++ b/share/top/amber03.ff/aminoacids.r2b @@ -18,7 +18,7 @@ PHE PHE NPHE CPHE PHE TYR TYR NTYR CTYR TYR GLU GLU NGLU CGLU GLU ASP ASP NASP CASP ASP -LYS LYP NLYP CLYP LYP +LYS LYS NLYS CLYS LYS ORN ORN NORN CORN ORN DAB DAB NDAB CDAB DAB LYSN LYN NLYN CLYN LYN diff --git a/share/top/amber03.ff/aminoacids.rtp b/share/top/amber03.ff/aminoacids.rtp index 2d93a77f1c..99122d0ef6 100644 --- a/share/top/amber03.ff/aminoacids.rtp +++ b/share/top/amber03.ff/aminoacids.rtp @@ -976,7 +976,7 @@ CA +N C O CB OD1 CG OD2 -[ LYP ] +[ LYS ] [ atoms ] N N -0.435875 1 H H 0.251302 2 @@ -2265,7 +2265,7 @@ CA OC1 C OC2 CB OD1 CG OD2 -[ CLYP ] +[ CLYS ] [ atoms ] N N -0.34810 1 H H 0.27640 2 @@ -3281,7 +3281,7 @@ CA +N C O CB OD1 CG OD2 -[ NLYP ] +[ NLYS ] [ atoms ] N N3 0.09660 1 H1 H 0.21650 2 diff --git a/share/top/amber94.ff/aminoacids.arn b/share/top/amber94.ff/aminoacids.arn index 333fa567e6..253f8ba6f2 100644 --- a/share/top/amber94.ff/aminoacids.arn +++ b/share/top/amber94.ff/aminoacids.arn @@ -18,7 +18,7 @@ NTYR H H1 NGLU H H1 NASP H H1 - NLYP H H1 + NLYS H H1 NPRO H H1 NCYN H H1 NCYX H H1 @@ -65,8 +65,8 @@ CGLU OXT OC1 CASP O OC2 CASP OXT OC1 - CLYP O OC2 - CLYP OXT OC1 + CLYS O OC2 + CLYS OXT OC1 CPRO O OC2 CPRO OXT OC1 CCYN O OC2 diff --git a/share/top/amber94.ff/aminoacids.hdb b/share/top/amber94.ff/aminoacids.hdb index 6975ca41e6..90cb8582e8 100644 --- a/share/top/amber94.ff/aminoacids.hdb +++ b/share/top/amber94.ff/aminoacids.hdb @@ -128,7 +128,7 @@ ASP 3 1 1 H N -C CA 1 5 HA CA N CB C 2 6 HB CB CA CG -LYP 7 +LYS 7 1 1 H N -C CA 1 5 HA CA N CB C 2 6 HB CB CA CG @@ -337,7 +337,7 @@ CASP 4 1 5 HA CA N CB C 2 6 HB CB CA CG 1 1 OC1 C CA OC2 -CLYP 8 +CLYS 8 1 1 H N -C CA 1 5 HA CA N CB C 2 6 HB CB CA CG @@ -487,7 +487,7 @@ NASP 3 3 4 H N CA CB 1 5 HA CA N CB C 2 6 HB CB CA CG -NLYP 7 +NLYS 7 3 4 H N CA CB 1 5 HA CA N CB C 2 6 HB CB CA CG diff --git a/share/top/amber94.ff/aminoacids.r2b b/share/top/amber94.ff/aminoacids.r2b index 48422d81dc..22ac11c6e4 100644 --- a/share/top/amber94.ff/aminoacids.r2b +++ b/share/top/amber94.ff/aminoacids.r2b @@ -18,7 +18,7 @@ PHE PHE NPHE CPHE PHE TYR TYR NTYR CTYR TYR GLU GLU NGLU CGLU GLU ASP ASP NASP CASP ASP -LYS LYP NLYP CLYP LYP +LYS LYS NLYS CLYS LYS ORN ORN NORN CORN ORN DAB DAB NDAB CDAB DAB LYSN LYN NLYN CLYN LYN diff --git a/share/top/amber94.ff/aminoacids.rtp b/share/top/amber94.ff/aminoacids.rtp index 23511a3852..2a76e5a2b1 100644 --- a/share/top/amber94.ff/aminoacids.rtp +++ b/share/top/amber94.ff/aminoacids.rtp @@ -10,9 +10,9 @@ ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih 1 1 9 4 1 3 1 0 -; first are tip3p, heavy tip3p, tip4p, tip4p-EW, and tip5p; then ion definitions, urea, and terminal caps +; now: water, ions, urea, terminal caps, AA's and terminal AA's -;tip3p +; tip3p [ HOH ] [ atoms ] OW OW -0.834 0 @@ -22,55 +22,13 @@ OW HW1 OW HW2 -[ T3P ] +; tip4p +[ HO4 ] [ atoms ] - OW OW -0.834 0 - HW1 HW 0.417 0 - HW2 HW 0.417 0 - [ bonds ] - OW HW1 - OW HW2 - -;tip3p (heavy) -[ T3H ] - [ atoms ] - OW OW_tip3p -0.834 0 - HW1 HW_tip3p 0.417 0 - HW2 HW_tip3p 0.417 0 - [ bonds ] - OW HW1 - OW HW2 - -;tip4p -[ T4P ] - [ atoms ] - OW OW_tip4p 0.000 0 - HW2 HW_tip4p 0.520 0 - HW3 HW_tip4p 0.520 0 - MW4 MW -1.040 0 - [ bonds ] - OW HW1 - OW HW2 - -;tip4p-EW -[ T4E ] - [ atoms ] - OW OW_tip4pew 0.000 0 - HW1 HW_tip4pew 0.52422 0 - HW2 HW_tip4pew 0.52422 0 - MW MW -1.04844 0 - [ bonds ] - OW HW1 - OW HW2 - -;tip5p -[ T5P ] - [ atoms ] - OW OW_tip5p 0.000 0 - HW1 HW_tip5p 0.241 0 - HW2 HW_tip5p 0.241 0 - LP1 MW -0.241 0 - LP2 MW -0.241 0 + OW OW_tip4p 0.00 0 + HW1 HW 0.52 0 + HW2 HW 0.52 0 + MW MW -1.04 0 [ bonds ] OW HW1 OW HW2 @@ -964,7 +922,7 @@ CA +N C O CB OD1 CG OD2 -[ LYP ] +[ LYS ] [ atoms ] N N -0.34790 1 H H 0.27470 2 @@ -2252,7 +2210,7 @@ CA OC1 C OC2 CB OD1 CG OD2 -[ CLYP ] +[ CLYS ] [ atoms ] N N -0.34810 1 H H 0.27640 2 @@ -3268,7 +3226,7 @@ CA +N C O CB OD1 CG OD2 -[ NLYP ] +[ NLYS ] [ atoms ] N N3 0.09660 1 H1 H 0.21650 2 diff --git a/share/top/amber96.ff/aminoacids.arn b/share/top/amber96.ff/aminoacids.arn index 333fa567e6..253f8ba6f2 100644 --- a/share/top/amber96.ff/aminoacids.arn +++ b/share/top/amber96.ff/aminoacids.arn @@ -18,7 +18,7 @@ NTYR H H1 NGLU H H1 NASP H H1 - NLYP H H1 + NLYS H H1 NPRO H H1 NCYN H H1 NCYX H H1 @@ -65,8 +65,8 @@ CGLU OXT OC1 CASP O OC2 CASP OXT OC1 - CLYP O OC2 - CLYP OXT OC1 + CLYS O OC2 + CLYS OXT OC1 CPRO O OC2 CPRO OXT OC1 CCYN O OC2 diff --git a/share/top/amber96.ff/aminoacids.hdb b/share/top/amber96.ff/aminoacids.hdb index 6975ca41e6..90cb8582e8 100644 --- a/share/top/amber96.ff/aminoacids.hdb +++ b/share/top/amber96.ff/aminoacids.hdb @@ -128,7 +128,7 @@ ASP 3 1 1 H N -C CA 1 5 HA CA N CB C 2 6 HB CB CA CG -LYP 7 +LYS 7 1 1 H N -C CA 1 5 HA CA N CB C 2 6 HB CB CA CG @@ -337,7 +337,7 @@ CASP 4 1 5 HA CA N CB C 2 6 HB CB CA CG 1 1 OC1 C CA OC2 -CLYP 8 +CLYS 8 1 1 H N -C CA 1 5 HA CA N CB C 2 6 HB CB CA CG @@ -487,7 +487,7 @@ NASP 3 3 4 H N CA CB 1 5 HA CA N CB C 2 6 HB CB CA CG -NLYP 7 +NLYS 7 3 4 H N CA CB 1 5 HA CA N CB C 2 6 HB CB CA CG diff --git a/share/top/amber96.ff/aminoacids.r2b b/share/top/amber96.ff/aminoacids.r2b index 48422d81dc..22ac11c6e4 100644 --- a/share/top/amber96.ff/aminoacids.r2b +++ b/share/top/amber96.ff/aminoacids.r2b @@ -18,7 +18,7 @@ PHE PHE NPHE CPHE PHE TYR TYR NTYR CTYR TYR GLU GLU NGLU CGLU GLU ASP ASP NASP CASP ASP -LYS LYP NLYP CLYP LYP +LYS LYS NLYS CLYS LYS ORN ORN NORN CORN ORN DAB DAB NDAB CDAB DAB LYSN LYN NLYN CLYN LYN diff --git a/share/top/amber96.ff/aminoacids.rtp b/share/top/amber96.ff/aminoacids.rtp index 23511a3852..2a76e5a2b1 100644 --- a/share/top/amber96.ff/aminoacids.rtp +++ b/share/top/amber96.ff/aminoacids.rtp @@ -10,9 +10,9 @@ ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih 1 1 9 4 1 3 1 0 -; first are tip3p, heavy tip3p, tip4p, tip4p-EW, and tip5p; then ion definitions, urea, and terminal caps +; now: water, ions, urea, terminal caps, AA's and terminal AA's -;tip3p +; tip3p [ HOH ] [ atoms ] OW OW -0.834 0 @@ -22,55 +22,13 @@ OW HW1 OW HW2 -[ T3P ] +; tip4p +[ HO4 ] [ atoms ] - OW OW -0.834 0 - HW1 HW 0.417 0 - HW2 HW 0.417 0 - [ bonds ] - OW HW1 - OW HW2 - -;tip3p (heavy) -[ T3H ] - [ atoms ] - OW OW_tip3p -0.834 0 - HW1 HW_tip3p 0.417 0 - HW2 HW_tip3p 0.417 0 - [ bonds ] - OW HW1 - OW HW2 - -;tip4p -[ T4P ] - [ atoms ] - OW OW_tip4p 0.000 0 - HW2 HW_tip4p 0.520 0 - HW3 HW_tip4p 0.520 0 - MW4 MW -1.040 0 - [ bonds ] - OW HW1 - OW HW2 - -;tip4p-EW -[ T4E ] - [ atoms ] - OW OW_tip4pew 0.000 0 - HW1 HW_tip4pew 0.52422 0 - HW2 HW_tip4pew 0.52422 0 - MW MW -1.04844 0 - [ bonds ] - OW HW1 - OW HW2 - -;tip5p -[ T5P ] - [ atoms ] - OW OW_tip5p 0.000 0 - HW1 HW_tip5p 0.241 0 - HW2 HW_tip5p 0.241 0 - LP1 MW -0.241 0 - LP2 MW -0.241 0 + OW OW_tip4p 0.00 0 + HW1 HW 0.52 0 + HW2 HW 0.52 0 + MW MW -1.04 0 [ bonds ] OW HW1 OW HW2 @@ -964,7 +922,7 @@ CA +N C O CB OD1 CG OD2 -[ LYP ] +[ LYS ] [ atoms ] N N -0.34790 1 H H 0.27470 2 @@ -2252,7 +2210,7 @@ CA OC1 C OC2 CB OD1 CG OD2 -[ CLYP ] +[ CLYS ] [ atoms ] N N -0.34810 1 H H 0.27640 2 @@ -3268,7 +3226,7 @@ CA +N C O CB OD1 CG OD2 -[ NLYP ] +[ NLYS ] [ atoms ] N N3 0.09660 1 H1 H 0.21650 2 diff --git a/share/top/amber99.ff/aminoacids.arn b/share/top/amber99.ff/aminoacids.arn index 297dd9cbe6..8d33a3b54d 100644 --- a/share/top/amber99.ff/aminoacids.arn +++ b/share/top/amber99.ff/aminoacids.arn @@ -18,7 +18,7 @@ NTYR H H1 NGLU H H1 NASP H H1 - NLYP H H1 + NLYS H H1 NPRO H H1 NCYN H H1 NCYX H H1 @@ -65,8 +65,8 @@ CGLU OXT OC1 CASP O OC2 CASP OXT OC1 - CLYP O OC2 - CLYP OXT OC1 + CLYS O OC2 + CLYS OXT OC1 CPRO O OC2 CPRO OXT OC1 CCYN O OC2 diff --git a/share/top/amber99.ff/aminoacids.hdb b/share/top/amber99.ff/aminoacids.hdb index 6975ca41e6..90cb8582e8 100644 --- a/share/top/amber99.ff/aminoacids.hdb +++ b/share/top/amber99.ff/aminoacids.hdb @@ -128,7 +128,7 @@ ASP 3 1 1 H N -C CA 1 5 HA CA N CB C 2 6 HB CB CA CG -LYP 7 +LYS 7 1 1 H N -C CA 1 5 HA CA N CB C 2 6 HB CB CA CG @@ -337,7 +337,7 @@ CASP 4 1 5 HA CA N CB C 2 6 HB CB CA CG 1 1 OC1 C CA OC2 -CLYP 8 +CLYS 8 1 1 H N -C CA 1 5 HA CA N CB C 2 6 HB CB CA CG @@ -487,7 +487,7 @@ NASP 3 3 4 H N CA CB 1 5 HA CA N CB C 2 6 HB CB CA CG -NLYP 7 +NLYS 7 3 4 H N CA CB 1 5 HA CA N CB C 2 6 HB CB CA CG diff --git a/share/top/amber99.ff/aminoacids.r2b b/share/top/amber99.ff/aminoacids.r2b index 48422d81dc..22ac11c6e4 100644 --- a/share/top/amber99.ff/aminoacids.r2b +++ b/share/top/amber99.ff/aminoacids.r2b @@ -18,7 +18,7 @@ PHE PHE NPHE CPHE PHE TYR TYR NTYR CTYR TYR GLU GLU NGLU CGLU GLU ASP ASP NASP CASP ASP -LYS LYP NLYP CLYP LYP +LYS LYS NLYS CLYS LYS ORN ORN NORN CORN ORN DAB DAB NDAB CDAB DAB LYSN LYN NLYN CLYN LYN diff --git a/share/top/amber99.ff/aminoacids.rtp b/share/top/amber99.ff/aminoacids.rtp index 91b61c36c4..dbbffc2192 100644 --- a/share/top/amber99.ff/aminoacids.rtp +++ b/share/top/amber99.ff/aminoacids.rtp @@ -10,9 +10,9 @@ ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih 1 1 9 4 1 3 1 0 -; first are tip3p, heavy tip3p, tip4p, tip4p-EW, and tip5p; then ion definitions, urea, and terminal caps +; now: water, ions, urea, terminal caps, AA's and terminal AA's -;tip3p +; tip3p [ HOH ] [ atoms ] OW OW -0.834 0 @@ -22,55 +22,13 @@ OW HW1 OW HW2 -[ T3P ] +; tip4p +[ HO4 ] [ atoms ] - OW OW -0.834 0 - HW1 HW 0.417 0 - HW2 HW 0.417 0 - [ bonds ] - OW HW1 - OW HW2 - -;tip3p (heavy) -[ T3H ] - [ atoms ] - OW OW_tip3p -0.834 0 - HW1 HW_tip3p 0.417 0 - HW2 HW_tip3p 0.417 0 - [ bonds ] - OW HW1 - OW HW2 - -;tip4p -[ T4P ] - [ atoms ] - OW OW_tip4p 0.000 0 - HW2 HW_tip4p 0.520 0 - HW3 HW_tip4p 0.520 0 - MW4 MW -1.040 0 - [ bonds ] - OW HW1 - OW HW2 - -;tip4p-EW -[ T4E ] - [ atoms ] - OW OW_tip4pew 0.000 0 - HW1 HW_tip4pew 0.52422 0 - HW2 HW_tip4pew 0.52422 0 - MW MW -1.04844 0 - [ bonds ] - OW HW1 - OW HW2 - -;tip5p -[ T5P ] - [ atoms ] - OW OW_tip5p 0.000 0 - HW1 HW_tip5p 0.241 0 - HW2 HW_tip5p 0.241 0 - LP1 MW -0.241 0 - LP2 MW -0.241 0 + OW OW_tip4p 0.00 0 + HW1 HW 0.52 0 + HW2 HW 0.52 0 + MW MW -1.04 0 [ bonds ] OW HW1 OW HW2 @@ -113,11 +71,11 @@ [ Zn+ ] [ atoms ] - Zn Zn 2.00000 1 + Zn Zn 2.00000 1 -[ URE ] ; added in by EJS, resp charges by Jim Caldwell +[ URE ] ; urea added in by EJS, resp charges by Jim Caldwell [ atoms ] - C C 0.880229 1 + C C 0.880229 1 O O -0.613359 2 N1 N -0.923545 3 H11 H 0.395055 4 @@ -134,7 +92,7 @@ N2 H21 N2 H22 [ impropers ] - N1 N2 C O + N1 N2 C O C H11 N1 H12 C H21 N2 H22 @@ -964,7 +922,7 @@ CA +N C O CB OD1 CG OD2 -[ LYP ] +[ LYS ] [ atoms ] N N -0.34790 1 H H 0.27470 2 @@ -2253,7 +2211,7 @@ CA OC1 C OC2 CB OD1 CG OD2 -[ CLYP ] +[ CLYS ] [ atoms ] N N -0.34810 1 H H 0.27640 2 @@ -3269,7 +3227,7 @@ CA +N C O CB OD1 CG OD2 -[ NLYP ] +[ NLYS ] [ atoms ] N N3 0.09660 1 H1 H 0.21650 2 diff --git a/share/top/amber99sb-ildn.ff/aminoacids.arn b/share/top/amber99sb-ildn.ff/aminoacids.arn index 333fa567e6..253f8ba6f2 100644 --- a/share/top/amber99sb-ildn.ff/aminoacids.arn +++ b/share/top/amber99sb-ildn.ff/aminoacids.arn @@ -18,7 +18,7 @@ NTYR H H1 NGLU H H1 NASP H H1 - NLYP H H1 + NLYS H H1 NPRO H H1 NCYN H H1 NCYX H H1 @@ -65,8 +65,8 @@ CGLU OXT OC1 CASP O OC2 CASP OXT OC1 - CLYP O OC2 - CLYP OXT OC1 + CLYS O OC2 + CLYS OXT OC1 CPRO O OC2 CPRO OXT OC1 CCYN O OC2 diff --git a/share/top/amber99sb-ildn.ff/aminoacids.hdb b/share/top/amber99sb-ildn.ff/aminoacids.hdb index 6975ca41e6..90cb8582e8 100644 --- a/share/top/amber99sb-ildn.ff/aminoacids.hdb +++ b/share/top/amber99sb-ildn.ff/aminoacids.hdb @@ -128,7 +128,7 @@ ASP 3 1 1 H N -C CA 1 5 HA CA N CB C 2 6 HB CB CA CG -LYP 7 +LYS 7 1 1 H N -C CA 1 5 HA CA N CB C 2 6 HB CB CA CG @@ -337,7 +337,7 @@ CASP 4 1 5 HA CA N CB C 2 6 HB CB CA CG 1 1 OC1 C CA OC2 -CLYP 8 +CLYS 8 1 1 H N -C CA 1 5 HA CA N CB C 2 6 HB CB CA CG @@ -487,7 +487,7 @@ NASP 3 3 4 H N CA CB 1 5 HA CA N CB C 2 6 HB CB CA CG -NLYP 7 +NLYS 7 3 4 H N CA CB 1 5 HA CA N CB C 2 6 HB CB CA CG diff --git a/share/top/amber99sb-ildn.ff/aminoacids.r2b b/share/top/amber99sb-ildn.ff/aminoacids.r2b index 48422d81dc..22ac11c6e4 100644 --- a/share/top/amber99sb-ildn.ff/aminoacids.r2b +++ b/share/top/amber99sb-ildn.ff/aminoacids.r2b @@ -18,7 +18,7 @@ PHE PHE NPHE CPHE PHE TYR TYR NTYR CTYR TYR GLU GLU NGLU CGLU GLU ASP ASP NASP CASP ASP -LYS LYP NLYP CLYP LYP +LYS LYS NLYS CLYS LYS ORN ORN NORN CORN ORN DAB DAB NDAB CDAB DAB LYSN LYN NLYN CLYN LYN diff --git a/share/top/amber99sb-ildn.ff/aminoacids.rtp b/share/top/amber99sb-ildn.ff/aminoacids.rtp index 697dbb2cf5..6fd391b0a4 100644 --- a/share/top/amber99sb-ildn.ff/aminoacids.rtp +++ b/share/top/amber99sb-ildn.ff/aminoacids.rtp @@ -10,9 +10,9 @@ ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih 1 1 9 4 1 3 1 0 -; first are tip3p, heavy tip3p, tip4p, tip4p-EW, and tip5p; then ion definitions, urea, and terminal caps +; now: water, ions, urea, terminal caps, AA's and terminal AA's -;tip3p +; tip3p [ HOH ] [ atoms ] OW OW -0.834 0 @@ -22,55 +22,13 @@ OW HW1 OW HW2 -[ T3P ] +; tip4p +[ HO4 ] [ atoms ] - OW OW -0.834 0 - HW1 HW 0.417 0 - HW2 HW 0.417 0 - [ bonds ] - OW HW1 - OW HW2 - -;tip3p (heavy) -[ T3H ] - [ atoms ] - OW OW_tip3p -0.834 0 - HW1 HW_tip3p 0.417 0 - HW2 HW_tip3p 0.417 0 - [ bonds ] - OW HW1 - OW HW2 - -;tip4p -[ T4P ] - [ atoms ] - OW OW_tip4p 0.000 0 - HW2 HW_tip4p 0.520 0 - HW3 HW_tip4p 0.520 0 - MW4 MW -1.040 0 - [ bonds ] - OW HW1 - OW HW2 - -;tip4p-EW -[ T4E ] - [ atoms ] - OW OW_tip4pew 0.000 0 - HW1 HW_tip4pew 0.52422 0 - HW2 HW_tip4pew 0.52422 0 - MW MW -1.04844 0 - [ bonds ] - OW HW1 - OW HW2 - -;tip5p -[ T5P ] - [ atoms ] - OW OW_tip5p 0.000 0 - HW1 HW_tip5p 0.241 0 - HW2 HW_tip5p 0.241 0 - LP1 MW -0.241 0 - LP2 MW -0.241 0 + OW OW_tip4p 0.00 0 + HW1 HW 0.52 0 + HW2 HW 0.52 0 + MW MW -1.04 0 [ bonds ] OW HW1 OW HW2 @@ -113,11 +71,11 @@ [ Zn+ ] [ atoms ] - Zn Zn 2.00000 1 + Zn Zn 2.00000 1 -[ URE ] ; added in by EJS, resp charges by Jim Caldwell +[ URE ] ; urea added in by EJS, resp charges by Jim Caldwell [ atoms ] - C C 0.880229 1 + C C 0.880229 1 O O -0.613359 2 N1 N -0.923545 3 H11 H 0.395055 4 @@ -134,7 +92,7 @@ N2 H21 N2 H22 [ impropers ] - N1 N2 C O + N1 N2 C O C H11 N1 H12 C H21 N2 H22 @@ -1003,7 +961,7 @@ CA +N C O CB OD1 CG OD2 -[ LYP ] +[ LYS ] [ atoms ] N N -0.34790 1 H H 0.27470 2 @@ -2331,7 +2289,7 @@ CA OC1 C OC2 CB OD1 CG OD2 -[ CLYP ] +[ CLYS ] [ atoms ] N N -0.34810 1 H H 0.27640 2 @@ -2702,7 +2660,6 @@ C CA CB CG torsion_LEU_C_CA_CB_CG_mult3 [ impropers ] CA +N C O - [ NILE ] [ atoms ] @@ -3387,7 +3344,7 @@ CA +N C O CB OD1 CG OD2 -[ NLYP ] +[ NLYS ] [ atoms ] N N3 0.09660 1 H1 H 0.21650 2 diff --git a/share/top/amber99sb.ff/aminoacids.arn b/share/top/amber99sb.ff/aminoacids.arn index 333fa567e6..253f8ba6f2 100644 --- a/share/top/amber99sb.ff/aminoacids.arn +++ b/share/top/amber99sb.ff/aminoacids.arn @@ -18,7 +18,7 @@ NTYR H H1 NGLU H H1 NASP H H1 - NLYP H H1 + NLYS H H1 NPRO H H1 NCYN H H1 NCYX H H1 @@ -65,8 +65,8 @@ CGLU OXT OC1 CASP O OC2 CASP OXT OC1 - CLYP O OC2 - CLYP OXT OC1 + CLYS O OC2 + CLYS OXT OC1 CPRO O OC2 CPRO OXT OC1 CCYN O OC2 diff --git a/share/top/amber99sb.ff/aminoacids.hdb b/share/top/amber99sb.ff/aminoacids.hdb index 6975ca41e6..90cb8582e8 100644 --- a/share/top/amber99sb.ff/aminoacids.hdb +++ b/share/top/amber99sb.ff/aminoacids.hdb @@ -128,7 +128,7 @@ ASP 3 1 1 H N -C CA 1 5 HA CA N CB C 2 6 HB CB CA CG -LYP 7 +LYS 7 1 1 H N -C CA 1 5 HA CA N CB C 2 6 HB CB CA CG @@ -337,7 +337,7 @@ CASP 4 1 5 HA CA N CB C 2 6 HB CB CA CG 1 1 OC1 C CA OC2 -CLYP 8 +CLYS 8 1 1 H N -C CA 1 5 HA CA N CB C 2 6 HB CB CA CG @@ -487,7 +487,7 @@ NASP 3 3 4 H N CA CB 1 5 HA CA N CB C 2 6 HB CB CA CG -NLYP 7 +NLYS 7 3 4 H N CA CB 1 5 HA CA N CB C 2 6 HB CB CA CG diff --git a/share/top/amber99sb.ff/aminoacids.r2b b/share/top/amber99sb.ff/aminoacids.r2b index 48422d81dc..22ac11c6e4 100644 --- a/share/top/amber99sb.ff/aminoacids.r2b +++ b/share/top/amber99sb.ff/aminoacids.r2b @@ -18,7 +18,7 @@ PHE PHE NPHE CPHE PHE TYR TYR NTYR CTYR TYR GLU GLU NGLU CGLU GLU ASP ASP NASP CASP ASP -LYS LYP NLYP CLYP LYP +LYS LYS NLYS CLYS LYS ORN ORN NORN CORN ORN DAB DAB NDAB CDAB DAB LYSN LYN NLYN CLYN LYN diff --git a/share/top/amber99sb.ff/aminoacids.rtp b/share/top/amber99sb.ff/aminoacids.rtp index 91b61c36c4..dbbffc2192 100644 --- a/share/top/amber99sb.ff/aminoacids.rtp +++ b/share/top/amber99sb.ff/aminoacids.rtp @@ -10,9 +10,9 @@ ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih 1 1 9 4 1 3 1 0 -; first are tip3p, heavy tip3p, tip4p, tip4p-EW, and tip5p; then ion definitions, urea, and terminal caps +; now: water, ions, urea, terminal caps, AA's and terminal AA's -;tip3p +; tip3p [ HOH ] [ atoms ] OW OW -0.834 0 @@ -22,55 +22,13 @@ OW HW1 OW HW2 -[ T3P ] +; tip4p +[ HO4 ] [ atoms ] - OW OW -0.834 0 - HW1 HW 0.417 0 - HW2 HW 0.417 0 - [ bonds ] - OW HW1 - OW HW2 - -;tip3p (heavy) -[ T3H ] - [ atoms ] - OW OW_tip3p -0.834 0 - HW1 HW_tip3p 0.417 0 - HW2 HW_tip3p 0.417 0 - [ bonds ] - OW HW1 - OW HW2 - -;tip4p -[ T4P ] - [ atoms ] - OW OW_tip4p 0.000 0 - HW2 HW_tip4p 0.520 0 - HW3 HW_tip4p 0.520 0 - MW4 MW -1.040 0 - [ bonds ] - OW HW1 - OW HW2 - -;tip4p-EW -[ T4E ] - [ atoms ] - OW OW_tip4pew 0.000 0 - HW1 HW_tip4pew 0.52422 0 - HW2 HW_tip4pew 0.52422 0 - MW MW -1.04844 0 - [ bonds ] - OW HW1 - OW HW2 - -;tip5p -[ T5P ] - [ atoms ] - OW OW_tip5p 0.000 0 - HW1 HW_tip5p 0.241 0 - HW2 HW_tip5p 0.241 0 - LP1 MW -0.241 0 - LP2 MW -0.241 0 + OW OW_tip4p 0.00 0 + HW1 HW 0.52 0 + HW2 HW 0.52 0 + MW MW -1.04 0 [ bonds ] OW HW1 OW HW2 @@ -113,11 +71,11 @@ [ Zn+ ] [ atoms ] - Zn Zn 2.00000 1 + Zn Zn 2.00000 1 -[ URE ] ; added in by EJS, resp charges by Jim Caldwell +[ URE ] ; urea added in by EJS, resp charges by Jim Caldwell [ atoms ] - C C 0.880229 1 + C C 0.880229 1 O O -0.613359 2 N1 N -0.923545 3 H11 H 0.395055 4 @@ -134,7 +92,7 @@ N2 H21 N2 H22 [ impropers ] - N1 N2 C O + N1 N2 C O C H11 N1 H12 C H21 N2 H22 @@ -964,7 +922,7 @@ CA +N C O CB OD1 CG OD2 -[ LYP ] +[ LYS ] [ atoms ] N N -0.34790 1 H H 0.27470 2 @@ -2253,7 +2211,7 @@ CA OC1 C OC2 CB OD1 CG OD2 -[ CLYP ] +[ CLYS ] [ atoms ] N N -0.34810 1 H H 0.27640 2 @@ -3269,7 +3227,7 @@ CA +N C O CB OD1 CG OD2 -[ NLYP ] +[ NLYS ] [ atoms ] N N3 0.09660 1 H1 H 0.21650 2 diff --git a/share/top/amberGS.ff/aminoacids.arn b/share/top/amberGS.ff/aminoacids.arn index 333fa567e6..253f8ba6f2 100644 --- a/share/top/amberGS.ff/aminoacids.arn +++ b/share/top/amberGS.ff/aminoacids.arn @@ -18,7 +18,7 @@ NTYR H H1 NGLU H H1 NASP H H1 - NLYP H H1 + NLYS H H1 NPRO H H1 NCYN H H1 NCYX H H1 @@ -65,8 +65,8 @@ CGLU OXT OC1 CASP O OC2 CASP OXT OC1 - CLYP O OC2 - CLYP OXT OC1 + CLYS O OC2 + CLYS OXT OC1 CPRO O OC2 CPRO OXT OC1 CCYN O OC2 diff --git a/share/top/amberGS.ff/aminoacids.hdb b/share/top/amberGS.ff/aminoacids.hdb index 6975ca41e6..90cb8582e8 100644 --- a/share/top/amberGS.ff/aminoacids.hdb +++ b/share/top/amberGS.ff/aminoacids.hdb @@ -128,7 +128,7 @@ ASP 3 1 1 H N -C CA 1 5 HA CA N CB C 2 6 HB CB CA CG -LYP 7 +LYS 7 1 1 H N -C CA 1 5 HA CA N CB C 2 6 HB CB CA CG @@ -337,7 +337,7 @@ CASP 4 1 5 HA CA N CB C 2 6 HB CB CA CG 1 1 OC1 C CA OC2 -CLYP 8 +CLYS 8 1 1 H N -C CA 1 5 HA CA N CB C 2 6 HB CB CA CG @@ -487,7 +487,7 @@ NASP 3 3 4 H N CA CB 1 5 HA CA N CB C 2 6 HB CB CA CG -NLYP 7 +NLYS 7 3 4 H N CA CB 1 5 HA CA N CB C 2 6 HB CB CA CG diff --git a/share/top/amberGS.ff/aminoacids.r2b b/share/top/amberGS.ff/aminoacids.r2b index 48422d81dc..22ac11c6e4 100644 --- a/share/top/amberGS.ff/aminoacids.r2b +++ b/share/top/amberGS.ff/aminoacids.r2b @@ -18,7 +18,7 @@ PHE PHE NPHE CPHE PHE TYR TYR NTYR CTYR TYR GLU GLU NGLU CGLU GLU ASP ASP NASP CASP ASP -LYS LYP NLYP CLYP LYP +LYS LYS NLYS CLYS LYS ORN ORN NORN CORN ORN DAB DAB NDAB CDAB DAB LYSN LYN NLYN CLYN LYN diff --git a/share/top/amberGS.ff/aminoacids.rtp b/share/top/amberGS.ff/aminoacids.rtp index 91b61c36c4..8725bcc5df 100644 --- a/share/top/amberGS.ff/aminoacids.rtp +++ b/share/top/amberGS.ff/aminoacids.rtp @@ -10,9 +10,9 @@ ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih 1 1 9 4 1 3 1 0 -; first are tip3p, heavy tip3p, tip4p, tip4p-EW, and tip5p; then ion definitions, urea, and terminal caps +; now: water, ions, urea, terminal caps, AA's and terminal AA's -;tip3p +; tip3p [ HOH ] [ atoms ] OW OW -0.834 0 @@ -22,55 +22,13 @@ OW HW1 OW HW2 -[ T3P ] +; tip4p +[ HO4 ] [ atoms ] - OW OW -0.834 0 - HW1 HW 0.417 0 - HW2 HW 0.417 0 - [ bonds ] - OW HW1 - OW HW2 - -;tip3p (heavy) -[ T3H ] - [ atoms ] - OW OW_tip3p -0.834 0 - HW1 HW_tip3p 0.417 0 - HW2 HW_tip3p 0.417 0 - [ bonds ] - OW HW1 - OW HW2 - -;tip4p -[ T4P ] - [ atoms ] - OW OW_tip4p 0.000 0 - HW2 HW_tip4p 0.520 0 - HW3 HW_tip4p 0.520 0 - MW4 MW -1.040 0 - [ bonds ] - OW HW1 - OW HW2 - -;tip4p-EW -[ T4E ] - [ atoms ] - OW OW_tip4pew 0.000 0 - HW1 HW_tip4pew 0.52422 0 - HW2 HW_tip4pew 0.52422 0 - MW MW -1.04844 0 - [ bonds ] - OW HW1 - OW HW2 - -;tip5p -[ T5P ] - [ atoms ] - OW OW_tip5p 0.000 0 - HW1 HW_tip5p 0.241 0 - HW2 HW_tip5p 0.241 0 - LP1 MW -0.241 0 - LP2 MW -0.241 0 + OW OW_tip4p 0.00 0 + HW1 HW 0.52 0 + HW2 HW 0.52 0 + MW MW -1.04 0 [ bonds ] OW HW1 OW HW2 @@ -113,11 +71,11 @@ [ Zn+ ] [ atoms ] - Zn Zn 2.00000 1 + Zn Zn 2.00000 1 -[ URE ] ; added in by EJS, resp charges by Jim Caldwell +[ URE ] ; urea added in by EJS, resp charges by Jim Caldwell [ atoms ] - C C 0.880229 1 + C C 0.880229 1 O O -0.613359 2 N1 N -0.923545 3 H11 H 0.395055 4 @@ -964,7 +922,7 @@ CA +N C O CB OD1 CG OD2 -[ LYP ] +[ LYS ] [ atoms ] N N -0.34790 1 H H 0.27470 2 @@ -2253,7 +2211,7 @@ CA OC1 C OC2 CB OD1 CG OD2 -[ CLYP ] +[ CLYS ] [ atoms ] N N -0.34810 1 H H 0.27640 2 @@ -3269,7 +3227,7 @@ CA +N C O CB OD1 CG OD2 -[ NLYP ] +[ NLYS ] [ atoms ] N N3 0.09660 1 H1 H 0.21650 2 -- 2.11.4.GIT