[gmx-users] problems running grompp with protein-ligand complex

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Nov 27 08:36:57 CET 2008

Hi Fabrício,

> I've checked wikigromacs, but the solution given there, to simply erase the
> second default line does not suit me here. Once I do this, i mean, go to my
> ligand.itp file and put a ; before my default section, grompp does not
> recognize anymore that my ligand is there and gives out another error line.

Well, it's not like grompp is recognizing you have a ligand there
right now, is it? grompp doesn't reach the point where it realizes you
don't seem to have a ligand. It seems there's something wrong with the
topology. Better post ligand.itp, like Justin suggests, and also give
the error which occurs when you do comment out the defaults line in
the ligand topology.



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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