[gmx-users] on prodrug server

[Justin Lemkul]

On 4/29/16 9:52 AM, Brett wrote:
> Dear All,
>
>
> If prodrug server wrongly assign charge group for a ligand, then what should I do? For example, I have a charge group of -1 group, however prodrug server including more atoms for this charge group and make the net charge of this charge group 0 charge.
>

Protonation state is addressed in the PRODRG FAQ.  Read that and contact the 
PRODRG developers if you have problems; this is not a GROMACS issue.

If you're curious about PRODRG artifacts, read 
http://pubs.acs.org/doi/abs/10.1021/ci100335w

-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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