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

[David]

On Mon, 2003-06-16 at 18:40, jiri vondrasek wrote:
> chris
>  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

the error message already indicates that you have included the force
field file twice, once in your top and once in your itp (probably). Take
the one in of your itp file out.

> thanks
> jiri
> 
> 
> 
> 
> 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.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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