[gmx-users] Protein-Ligand

Justin Lemkul jalemkul at vt.edu
Tue May 16 16:11:10 CEST 2017

On 5/15/17 9:12 AM, RAHUL SURESH wrote:
> Dear Users
> I am tryjng to simulate protein ligand complex using charmm36ff for 100ns.
> I found the ligand moving away from the protein around 55ns. I don't think
> it s a pbc effect. Is there anything I have done wrong or Should I add any
> additional commands.?
> Await your valuable advice.

Watch the trajectory and see which interactions break first.  Then consider if 
your ligand topology needs refinement to deal with such interactions or if it's 
trying to sample some strained conformation that is incompatible with binding 
(suggesting an internal/dihedral problem).  Compare with available experimental 
data; some things just have weak affinity.

> PS: Will the ligand move out of protein if the protein is over curved after
> interaction?

What does "over curved" mean?



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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