[gmx-users] Query- Ligand topology

[Justin Lemkul]

On 3/15/15 6:50 AM, Priya Das wrote:
> Dear all,
>
> I am submitting a ligand with 45 HETATM PDB file in PRODRG, but i get a
> result with 46 HETATM.
> The main error is in the -NH group, the structure generated by PRODRG shows
> four valence for Nitrogen.

Changing protonation states is covered in the PRODRG FAQ.

> Is there any other tool/option for generating the topology?
>

For GROMOS, try ATB.  At the very least, you need to be carefully scrutinizing 
and re-optimizing the PRODRG charges and charge groups.  The output is generally 
not very accurate.  Never trust a black box with something so crucial :)

-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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