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

[Justin A. Lemkul]

Vitaly Chaban wrote:
> Hey, Shiyong -
> 
> I believe your problem is related to X2TOP usage rather than to a
> proper force field choice. I'd suggest to start with looking into N2T
> files for the below entries.
> 

The output posted is from pdb2gmx.  It is also unlikely that x2top would be of 
any use for a coordinate file containing protein and RNA, given the complexity 
of such molecules.

-Justin

> Cheers.
> 
> --
> Dr. Vitaly V. Chaban
> Rochester, U.S.A.
> 
> 
>>  I just tried G53a6 for protein-RNA simulation. But fatal error shows up.
>>
>> Opening library file /usr/share/gromacs/top//FF.dat
>>
>> Select the Force Field:
>>  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
>>
>> --
>> Shiyong Liu

-- 
========================================

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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