[gmx-users] Ligand hybridization

[Justin Lemkul]

On 7/5/16 10:50 AM, Chetan Puri wrote:
> I am trying to do a protein- ligand simulation.
>
> And the prodrg server provides the ligand out  put by completely removing
> the double bonds(making it saturated)
>
> So is there any way to do it.
>

See the PRODRG FAQ for dealing with incorrect protonation.  Then make sure you 
fix the PRODRG topology because the charges won't be right.  Or use a better 
server like ATB.

-Justin

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

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

==================================================