[gmx-users] Re: Problem with Amber99SB-ILDN ff

Justin Lemkul jalemkul at vt.edu
Wed Jul 10 12:46:50 CEST 2013

On 7/9/13 5:34 PM, Melchor S. wrote:
> Sorry for the misunderstanding. I should had explained it better.
> I know that is a zwitterionic residue, I have run several simulations with
> the same PDB and with other forcefields. ACPYPE does not work, I tried it
> yesterday, but I have to check it. Antechamber I don't know, I have to try
> it.
> Also I will try to find other related parameters, but I was searching
> without succes. Could you suggest me something?

I've suggested everything I know, which is basically the general story for any 
"new" molecule in a force field - look for existing parameters, and if they 
don't exist, parameterize the molecule in a manner compatible with the parent 
force field.



Justin A. Lemkul, Ph.D.
Postdoctoral Associate

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


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