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

[Farid Sa'adedin]

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
Summerhall
Edinburgh EH9 1QH
SCOTLAND