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

[Vitaly Chaban]

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