[gmx-users] Can I run an MD simulation without protein??

David spoel at xray.bmc.uu.se
Tue May 11 20:52:54 CEST 2004

On Tue, 2004-05-11 at 18:37, Scott Classen wrote:
> Hello GROMAC Community,
> I have a small molecule that I would like to do MD on (in a box full of 
> DMSO), and I have used PRODRG to get a starting *.gro and *.itp file 
> for my small molecule.
> These are the commands I run and I have included part of my log file so 
> that someone might be able to help me out.

> Fatal error: Group Protein not found in indexfile.

you have to edit the mdp file. you have apparently taken one from an
example or something like that. gromacs can be used for all kinds of

> Maybe you have non-default goups in your mdp file, while not using the 
> '-n' option of grompp.
> In that case use the '-n' option.
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>    Scott Classen, Ph.D.
>    ACS Postdoctoral Fellow
>    Department of Molecular & Cell Biology
>    University of California, Berkeley
>    237 Hildebrand Hall #3206
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>    LAB 510.643.9491
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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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