[gmx-users] Ligand Boron parameters

Justin Lemkul jalemkul at vt.edu
Mon May 8 21:37:30 CEST 2017

On 5/8/17 9:04 AM, Pedro Fernandes wrote:
> Good afternoon,
> I’m trying to do molecular dynamics (protein-ligand) with a ligand that has a boron atom.
> Can anyone help me or give me some information how can I do the parameterization of the ligand.

The details will depend on the force field you've chosen to use for the protein. 
  Factoring into that decision is how easy it will be to parametrize a ligand 
with boron, which none of the commonly used biomolecular force fields have. 
You'll be starting from absolute scratch with that atom type so you will want to 
be well versed in force field parametrization methods (beware: expert topic ahead).



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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