[gmx-users] ligand in vacuum trajectories (PRODRG)

Farid Sa'adedin fsaadedi at staffmail.ed.ac.uk
Thu Mar 2 14:06:12 CET 2006

Quoting Dariusz Plewczynski <darman at bioinfo.pl>:

> Dear Sirs,
> I have a problem with running the short simulation with GROMACS. I have
> a structure for a small ligand (drg.pdb after cleaning with PRODRG). For
> this ligand I have run PRODRG in order to get drg.gro file and drg.itp
> topology file. I have edited the drg.top in order to include drg.itp as
> #include. My goal is to run simulation in vacuum (no water) - with only
> ligand (!). No protein also. I have tried to run it but I am getting
> error message. It seem that GROMACS does not read my topology file. What
> I am doing wrong ?
> grompp -f em.mdp -c drg.gro -p drg.top -o drg.tpr
> Results:
> ....
> creating statusfile for 1 node...
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
> checking input for internal consistency...
> calling /lib/cpp...
> processing topology...
> Generated 1284 of the 1485 non-bonded parameter combinations
> processing coordinates...
> Fatal error: number of coordinates in coordinate file (drg.gro, 25)
>              does not match topology (drg.top, 0)

You need to input the itp file generated by PRODRG of your drug into 
your drg.top file.

do that by #include "/your filepathway/drg.itp"

> Regards
> Dariusz

Farid Sa'adedin
Membrane Biophysics Laboratory
Department of Veterinary Biomedical Sciences
College of Medicine & Veterinary Medicine
Royal (Dick) School of Veterinary Studies
University of Edinburgh
Edinburgh EH9 1QH

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