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

[Yafei Dai]

St�phane,
Thank you so much. I will try your suggestion.
Yafei

----- Original Message -----
From: steletch at jouy.inra.fr
Date: Wednesday, September 5, 2007 6:22 pm
Subject: Re: [gmx-users] How to use PRODRG to help new user do gromacs?

> 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 
> atomdefinitions 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,
> 
> St�phane T�letch�a
> 
> -- 
> St�phane T�letch�a, PhD.                  http://www.steletch.org
> Unit� Math�matique Informatique et G�nome 
> http://migale.jouy.inra.fr/migINRA, Domaine de Vilvert             
>     T�l : (33) 134 652 891
> 78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901
> 
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