[gmx-users] PRODRG -cgnr
jalemkul at vt.edu
Mon Jul 28 17:44:19 CEST 2014
On 7/28/14, 10:06 AM, Atila Petrosian wrote:
> Dear Justin
> Thanks for your quick answers.
> Based on your answers, what should Ido?
> You have more experience than me in these regards. What is your suggestion
> about my ligand molecule?
Gromos96 parametrization is predicated upon transferring pieces of molecules
into larger pieces. So you need to find a suitable model compound that has
known experimental target data; ideally heat of vaporization and free energy of
solvation. Such information is available for a compound like acethydrazide,
which takes care of the most complex part of your molecule. Tune the nonbonded
parameters to reproduce the experimental data, then refine the bonded parameters
as needed to reproduce, e.g. crystal data and torsional energy profiles. Then
you can import the new parameters into the whole molecule.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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