[gmx-users] Protein-ligand complex simulation and ATBserver file

Justin Lemkul jalemkul at vt.edu
Wed Dec 19 18:37:09 CET 2018

On Wed, Dec 19, 2018 at 4:34 AM Prasanth G, Research Scholar <
prasanthghanta at sssihl.edu.in> wrote:

> Dear Sir,
> I am running GROMACS 5.1.4 on a server.
> I had converted the protein(pdb2gro) using the latest GROMOS forcefield.
> As per your suggestion, I had downloaded the parameter files from ATB
> server. As per the readme file from the server (in the parameters folder),
> i had updated my topol.top like this and also included the extracted folder
> to the working directory on the server.
> ---
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
> ; Include ligand topology
> #include "jz4.itp"
> ; Include force field parameters
> #include "home/bio1/PG/gromos54a7_atb.ff/forcefield.itp"
Your #include statements are out of order. The #include statement for the
parent force field (the line above) should appear before anything else in
the topology, as it defines the atom types. The ffnonbonded.itp file does,
in fact, define CAro, which is a nonstandard type from ATB. I also suspect
that your specified PATH is lacking an initial / - note that full PATH
information is not necessary if the force field subdirectory is in $GMXLIB
or in the working directory.




Justin A. Lemkul, Ph.D.

Assistant Professor

Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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