[gmx-users] The charge of cofactor and ligand

Justin Lemkul jalemkul at vt.edu
Wed Sep 25 00:41:18 CEST 2013

On 9/24/13 7:16 AM, aixintiankong wrote:
> Dear prof.
>        The format of  parameters is convenient to the  software of Amber and not to gromacs. if i use the parameters i must use some tools to convert it to  the itp format for gromacs. so i use acpype to get itp format.
>       i just doubt that i use amber99sb for protein and AM1-BBC for ligand and resp charge for cofactor.  it looks like unprofessional and i don't know whether can affect the the MD . I do like this is right or not ?

The best method is to follow published protocols rather than trying make 
something up that you hope will be right.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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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