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

[lloyd riggs]

-
> Message: 1
> Date: Thu, 9 Dec 2010 23:16:21 -0500
> From: Vitaly Chaban <vvchaban at gmail.com>
> Subject: [gmx-users] Re: Which FF could be used for protein-RNA MD
> 	simulation in GROMACS?
> To: gmx-users at gromacs.org
> Message-ID:
> 	<AANLkTik995O98r7gm8-KLac0xuF9M3rb_43+31Afap7U at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> 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.
> 
> 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
> 
> 
> ------------------------------


Dear Shiyong Liu,

I have run across RNA/DNA .itp/.rtp files by searching (for a while) on the internet, a year or so back, which are/were compatable with the G53a6 FF.  Aside from that though, I don't remember which lab/site had them.  The same is true for lipid and carbohydrate .itp/.rtp libraries.

Stephan Watkins
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