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

[Liu Shiyong]

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
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Chinese Version:
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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
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