From b37c3c10dfb9616e92e42849cbff23134e0d2a5f Mon Sep 17 00:00:00 2001 From: Erik Lindahl Date: Sun, 22 Aug 2010 11:23:52 +0200 Subject: [PATCH] Amber force fields now pass validation. Beta status removed. --- share/top/amber03.ff/forcefield.doc | 2 +- share/top/amber94.ff/forcefield.doc | 2 +- share/top/amber96.ff/forcefield.doc | 2 +- share/top/amber99.ff/forcefield.doc | 2 +- share/top/amber99sb-ildn.ff/forcefield.doc | 25 ++++++++++++------------- share/top/amber99sb.ff/forcefield.doc | 2 +- share/top/amber99sb.ff/tip4pew.itp | 5 +++++ share/top/amber99sb.ff/watermodels.dat | 2 +- share/top/amberGS.ff/forcefield.doc | 2 +- share/top/charmm27.ff/forcefield.doc | 2 +- 10 files changed, 25 insertions(+), 21 deletions(-) rewrite share/top/amber99sb-ildn.ff/forcefield.doc (77%) diff --git a/share/top/amber03.ff/forcefield.doc b/share/top/amber03.ff/forcefield.doc index fbb0015d22..c87b62f6e2 100644 --- a/share/top/amber03.ff/forcefield.doc +++ b/share/top/amber03.ff/forcefield.doc @@ -1,4 +1,4 @@ -AMBER03_TEST_ONLY_DO_NOT_USE_FOR_PRODUCTION +AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) ******************************************************************** * The original ffamber ports were written by Eric J. Sorin, * diff --git a/share/top/amber94.ff/forcefield.doc b/share/top/amber94.ff/forcefield.doc index 286710e398..18191c32b1 100644 --- a/share/top/amber94.ff/forcefield.doc +++ b/share/top/amber94.ff/forcefield.doc @@ -1,4 +1,4 @@ -AMBER94_TEST_ONLY_DO_NOT_USE_FOR_PRODUCTION +AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) ******************************************************************** * The original ffamber ports were written by Eric J. Sorin, * diff --git a/share/top/amber96.ff/forcefield.doc b/share/top/amber96.ff/forcefield.doc index 5513c017dd..b6716fd40e 100644 --- a/share/top/amber96.ff/forcefield.doc +++ b/share/top/amber96.ff/forcefield.doc @@ -1,4 +1,4 @@ -AMBER96_TEST_ONLY_DO_NOT_USE_FOR_PRODUCTION +AMBER96 force field (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) ******************************************************************** * The original ffamber ports were written by Eric J. Sorin, * diff --git a/share/top/amber99.ff/forcefield.doc b/share/top/amber99.ff/forcefield.doc index 5c699338ad..bb0de58521 100644 --- a/share/top/amber99.ff/forcefield.doc +++ b/share/top/amber99.ff/forcefield.doc @@ -1,4 +1,4 @@ -AMBER99_TEST_ONLY_DO_NOT_USE_FOR_PRODUCTION +AMBER99 force field (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000) ******************************************************************** * The original ffamber ports were written by Eric J. Sorin, * diff --git a/share/top/amber99sb-ildn.ff/forcefield.doc b/share/top/amber99sb-ildn.ff/forcefield.doc dissimilarity index 77% index 69587ab0ce..628657d072 100644 --- a/share/top/amber99sb-ildn.ff/forcefield.doc +++ b/share/top/amber99sb-ildn.ff/forcefield.doc @@ -1,13 +1,12 @@ -AMBER99SB-ILDN_TEST_ONLY_DO_NOT_USE_FOR_PRODUCTION - -******************************************************************** -* The original ffamber ports were written by Eric J. Sorin, * -* CSU Long Beach, Dept. of Chem & Biochem, and have now been * -* integrated with the standard gromacs distribution. * -* (Please don't blame Eric for errors we might have introduced.) * -* For the implementation/validation, please read/cite: * -* Sorin & Pande (2005). Biophys. J. 88(4), 2472-2493. * -* For related material and updates, please consult * -* http://chemistry.csulb.edu/ffamber/ * -******************************************************************** - +AMBER99SB-ILDN force field (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) + +******************************************************************** +* Amber99sb-ildn is an improvement to Amber99SB by * +* Kresten Lindorff-Larsen and coworkers at D.E. Shaw Research, inc.* +* The primary publication (please cite it) is * +* Lindorff-Larsen, K., Piana, S., Palmo, K., Maragakis, P., * +* Klepeis, J.L., Dror, R.O., Shaw, D.E., * +* Improved side-chain torsion potentials for the Amber ff99SB * +* protein force field, Proteins 78:1950–1958 (2010) * +******************************************************************** + diff --git a/share/top/amber99sb.ff/forcefield.doc b/share/top/amber99sb.ff/forcefield.doc index 5478ffdefc..a215227f77 100644 --- a/share/top/amber99sb.ff/forcefield.doc +++ b/share/top/amber99sb.ff/forcefield.doc @@ -1,4 +1,4 @@ -AMBER99SB_TEST_ONLY_DO_NOT_USE_FOR_PRODUCTION +AMBER99SB force field (Hornak et al., Proteins 65, 712-725, 2006) ******************************************************************** * The original ffamber ports were written by Eric J. Sorin, * diff --git a/share/top/amber99sb.ff/tip4pew.itp b/share/top/amber99sb.ff/tip4pew.itp index 571bec6444..13be1b3264 100644 --- a/share/top/amber99sb.ff/tip4pew.itp +++ b/share/top/amber99sb.ff/tip4pew.itp @@ -1,3 +1,8 @@ +; +; Horn et al. (2004). J. Chem. Phys.120, 9665-9678 +; + + [ moleculetype ] ; molname nrexcl SOL 2 diff --git a/share/top/amber99sb.ff/watermodels.dat b/share/top/amber99sb.ff/watermodels.dat index 420808db5e..66f8fabc0b 100644 --- a/share/top/amber99sb.ff/watermodels.dat +++ b/share/top/amber99sb.ff/watermodels.dat @@ -1,5 +1,5 @@ tip3p TIP3P TIP 3-point, recommended tip4p TIP4P TIP 4-point -tip4pew TIP4P-Ew TIP 4-point optimized with Ewald +tip4pew TIP4P-Ew TIP 4-point optimized with Ewald, recommended spc SPC simple point charge spce SPC/E extended simple point charge diff --git a/share/top/amberGS.ff/forcefield.doc b/share/top/amberGS.ff/forcefield.doc index 2c8b104e5f..df595982a6 100644 --- a/share/top/amberGS.ff/forcefield.doc +++ b/share/top/amberGS.ff/forcefield.doc @@ -1,4 +1,4 @@ -AMBERGS_TEST_ONLY_DO_NOT_USE_FOR_PRODUCTION +AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002) ******************************************************************** * The original ffamber ports were written by Eric J. Sorin, * diff --git a/share/top/charmm27.ff/forcefield.doc b/share/top/charmm27.ff/forcefield.doc index 5eac255fda..09dd7224b0 100644 --- a/share/top/charmm27.ff/forcefield.doc +++ b/share/top/charmm27.ff/forcefield.doc @@ -1,4 +1,4 @@ -CHARMM27 all-atom force field (with CMAP) - version 2.0beta +CHARMM27 all-atom force field (with CMAP) ****************************************************************** * Charmm to Gromacs port writted by * -- 2.11.4.GIT