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

[Yafei Dai]

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


----- Original Message -----
From: Yang Ye <leafyoung at yahoo.com>
Date: Wednesday, September 5, 2007 2:24 am
Subject: Re: [gmx-users] pdb file from prodrg2 cannot be recognized by gromacs?

> Hi,
> 
> You need to get the topology file from PRODRG together with the 
> PDB file 
> so you skip pdb2gmx and use the outputs from PRODRG in grompp 
> directly. 
> Of cource, do whatever you need to add water and ions before grompp.
> 
> Regards,
> Yang Ye
> 
> On 9/5/2007 10:51 AM, Yafei Dai wrote:
> > I got a pdb file from prodrg2 and I did pdb2gmx:
> >
> > pdb2gmx -f test.pdb -p test.top -o test.gro
> >
> > I was told "DRG" not found in residue topology. What can I do 
> for this error information? My pdb file is as below:
> >
> >
> >   
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