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

[Justin A. Lemkul]

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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