[gmx-users] new molecule with non standard residues and its solvation

jiri vondrasek jirka at uochb.cas.cz
Mon Jun 16 12:41:01 CEST 2003

 well, PRODRG says that file PDGGMX.TOP is an .itp file. The point I am
confused totaly  is pasted below.
I just followed the speptide manual up to the point where grompp is
taking place
well I got the following message at the end of the program run:
my command:
grompp -v -f em -c b4em -o em -p denda1

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Cleaning up temporary file gromppswhMTy
Fatal error: Found a second defaults directive, file
"/usr/local/share/gromacs/top/ffgmx.itp", line 6

will appreciate your opinion or telling me what is wrong

On Mon, 2003-06-16 at 05:43, Christoph Freudenberger wrote:
> jiri vondrasek wrote:
> > Hi all
> > I am quite unexperienced in GROMACS so the question is probably stupid.
> > I am trying to simulate a molecule with non standard residues (about
> > 300atoms) in solvent. The problem is that I do not know what kind and
> > number of files I need for successful gromacs run. I have already
> > created topology file and gro files at PRODRG. My question is - what's
> > next? I am reading gmx manual and some tutorials - unfortunately I was
> > not able to find any relevant information till now.Thanks
> If you already have the topology of the molecule you have to create
> a solvent box around it and get the simulation started.
> Check out the speptide tutorial. Your problem sounds quite similar.
> For further information about the options of the run input files
> refer to chapter 7 in the manual.
jiri vondrasek <jirka at uochb.cas.cz>

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