[gmx-users] including .itp file to system

Justin Lemkul jalemkul at vt.edu
Wed Dec 9 17:32:47 CET 2015

On 12/9/15 10:52 AM, Alex Mathew wrote:
> Hello everyone,
> i wanted to perform a Protein-Ligand Simulation,i created .itp,psf,.par etc
> files for ligand and am able to make topol.top and conf.gro or the protein
> using pdb2gmx .Forcefield is CHARMM27 Now i im confused how to include
> ligand into my system.as per tutorial we are provided with .gro file but in
> case of charmm forcefiled i didnt get any .gro file.

You don't need a .gro file; GROMACS happily accepts most coordinate formats. 
Probably .pdb is the most convenient for moving from CHARMM to GROMACS.

Or just upload everything to CHARMM-GUI and have it build the system and give 
you all the inputs you need.  Note that CHARMM27 is not a protein force field. 
What you're using is CHARMM22/CMAP.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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