[gmx-users] Ligand breaks during energy minimization

Justin Lemkul jalemkul at vt.edu
Fri Mar 25 12:48:28 CET 2016

On 3/24/16 8:35 PM, Soumya Lipsa Rath wrote:
> Dear gromacs users,
> I have a protein-ligand system to simulate. I got the parameters from
> CHARMM CGENFF and converted it to gromacs compatible parameters using
> "cgenff_charmm2gmx.py" script as Justin had suggested previously.
> Following the Protein-ligand tutorial of gromacs closely, I included the
> lig.itp and lig.prm file in my original only protein topology file,
> modified the output gro file making it a protein-ligand complex gro file.
> After solvation and addition of ions, when I am trying to run an energy
> minimization, my ligand breaks into pieces.
> Could anyone please give insights on what I might be doing wrong?

Try to minimize the ligand in vacuo, and in a box of water.  If those produce a 
distorted structure, you have a suboptimal topology.  Note that the stream file 
from CGenFF lists all penalty values; large values mean your work is not done! 
If the ligand minimizes properly in vacuo and in water, then the problem is with 
your construction of the complex (e.g. changes in coordinates, etc).



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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