[gmx-users] Which FF could be used for protein-RNA MD simulation in GROMACS?

Sat Dec 11 09:16:22 CET 2010

Sorry. Please skip my info. I found that the problem may be caused by bash .

 Now, it seems OK.

 Select the Force Field:
>From current directory:
 1: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
 3: AMBER96 force field (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
 4: AMBER99 force field (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
 5: AMBER99SB force field (Hornak et al., Proteins 65, 712-725, 2006)
 6: AMBER99SB-ILDN force field (Lindorff-Larsen et al., Proteins 78,
1950-58, 2010)
 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
 8: CHARMM27 all-atom force field (with CMAP) - version 2.0
 9: GROMOS96 43a1 force field
10: GROMOS96 43a2 force field (improved alkane dihedrals)
11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
14: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
15: [DEPRECATED] Encad all-atom force field, using full solvent charges
16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges
17: [DEPRECATED] Gromacs force field (see manual)
18: [DEPRECATED] Gromacs force field with hydrogens for NMR
>From '/usr/local/share/gromacs/top':
19: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
20: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
21: AMBER96 force field (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
22: AMBER99 force field (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
23: AMBER99SB force field (Hornak et al., Proteins 65, 712-725, 2006)
24: AMBER99SB-ILDN force field (Lindorff-Larsen et al., Proteins 78,
1950-58, 2010)
25: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
26: CHARMM27 all-atom force field (with CMAP) - version 2.0
27: GROMOS96 43a1 force field
28: GROMOS96 43a2 force field (improved alkane dihedrals)
29: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
30: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
31: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
32: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
33: [DEPRECATED] Encad all-atom force field, using full solvent charges
34: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges
35: [DEPRECATED] Gromacs force field (see manual)
36: [DEPRECATED] Gromacs force field with hydrogens for NMR

On Sat, Dec 11, 2010 at 4:05 PM, Liu Shiyong <liushiyong at gmail.com> wrote:
> I compiled the new version GROMACS 4.5.3
> and installed according to
> http://www.gromacs.org/Downloads/Installation_Instructions
>
> But I got the following info:
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.5.3
> Source code file: pdb2top.c, line: 154
>
> Fatal error:
> No force fields found (files with name 'forcefield.itp' in
> subdirectories ending on '.ff')
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> Thanx for Using GROMACS - Have a Nice Day
>
>
>
> On Fri, Dec 10, 2010 at 11:57 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>> Liu Shiyong wrote:
>>>
>>> Hi,
>>>
>>>  I just tried G53a6 for protein-RNA simulation. But fatal error shows up.
>>>
>>
>> That's a useless description of the problem.  Exact input and output would
>> be necessary to diagnose the problem.  Regardless, the choice of Gromos is a
>> particularly bad one for nucleic acid simulations.
>>
>> http://lists.gromacs.org/pipermail/gmx-users/2010-December/056409.html
>>
>>> Opening library file /usr/share/gromacs/top//FF.dat
>>>
>>> Select the Force Field:
>>
>> You probably don't want any of these force fields.  Ask yourself - what do
>> you commonly see in the literature?  Have similar studies been done?  I
>> would suggest upgrading to the latest version of Gromacs (4.5.3), which has
>> built-in compatibility with CHARMM many AMBER force fields.  Then do some
>> homework and decide.
>>
>> -Justin
>>
>>>  0: GROMOS96 43a1 force field
>>>  1: GROMOS96 43a2 force field (improved alkane dihedrals)
>>>  2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
>>>  3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
>>>  4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
>>>  5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>>>  6: [DEPRECATED] Gromacs force field (see manual)
>>>  7: [DEPRECATED] Gromacs force field with hydrogens for NMR
>>>  8: Encad all-atom force field, using scaled-down vacuum charges
>>>  9: Encad all-atom force field, using full solvent charges
>>>
>>> Best
>>>
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> --
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>
>
>
> --
> Shiyong Liu
> ------------------------------------------------------------------
> Biomolecular Physics and Modeling Group, Department of Physics,
> Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
> Tel：86-27-87558335-805
> ------------------------------------------------------------------
> Chinese Version:
> ------------------------------------------------------------------
> 刘士勇
> 华中科技大学物理学院  生物物理模建小组
> 湖北省武汉市洪山区珞瑜路1037号
> 邮编：430074
> 电话：86-27-87558335-805
> -------------------------------------------------------------------
>

-- 
Shiyong Liu
------------------------------------------------------------------
Biomolecular Physics and Modeling Group, Department of Physics,
Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
Tel：86-27-87558335-805
------------------------------------------------------------------
Chinese Version:
------------------------------------------------------------------
刘士勇
华中科技大学物理学院  生物物理模建小组
湖北省武汉市洪山区珞瑜路1037号
邮编：430074
电话：86-27-87558335-805
-------------------------------------------------------------------