[gmx-users] Query- Ligand parameterization

[Justin Lemkul]

On 3/25/15 3:24 PM, Priya Das wrote:
> Getting high penalty ligand. str generated by Paramchem. The suggestion is
> to do some validations. What steps are to be done to do these validations?
>

I linked the tutorial before.  That is the logic of the parametrization and a 
complete example.  If you need more help, you'll have to be specific about what 
the penalties are (charges? bonds? angles? dihedrals?).  If you parameters 
aren't very good, you'll need to run the required QM calculations yourself and 
fit the parameters to those target data.

-Justin

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

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