[gmx-users] How to use PRODRG to help new user do gromacs?

[steletch at jouy.inra.fr]

Selon Yafei Dai <ydai at gmu.edu>:

> Hi, all,
> I am a new user of gromacs and I read the manual and tutorial but I still get
> confused.
> I need your help.
>
> >From PRODRG, I got four *.top files, one *.itp file and three *.PDB files
> and some other files. In my system, I don't have any solvents, no any waters
> and no any ion.
>
> I take the "DRGCNS.TOP  : CNS topology file" and "DRGGMX.ITP  : GROMACS .itp
> file" and "DRGFIN.GRO  : final coordinates in GROMOS87 format" to gromacs and
> do "grompp -v", but I get error as below shows:
>
> Fatal error: number of coordinates in coordinate file (drgfin.gro, 15)
>              does not match topology (drgcns.top, 0)
>
> what can I do now? Thank you for you help.
> yafei

I presume you used the 'standard' proDRG, i strongly recommand to use the beta
version in order to get parameters for a 'correct' force-field, like for the
gromos96 and the like. By default (the 2.4 version of proDRG), the atom
definitions are provided for ffgmx (aka gromacs or gmx, which is now deprecated
as stated in the manual).

Please have a look at  http://wiki.gromacs.org/index.php/PRODRG for further
details.

Cheers,

Stéphane Téletchéa

-- 
Stéphane Téletchéa, PhD.                  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
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78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901