[gmx-users] PRODRG -cgnr

[Justin Lemkul]

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

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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