[gmx-users] The charge of cofactor and ligand

Justin Lemkul jalemkul at vt.edu
Tue Sep 24 03:26:15 CEST 2013

On 9/23/13 5:10 PM, aixintiankong wrote:
> Dear,
> First i use UCSF Chimera to add hydrogens and AM1-BCC charges for the NAD+ and a ligand. when i check  the charge of NAD+, I find that the distribution of charge is not correct, the N1N atom should be positive charge but the chimera give a negative. so i copy the resp charge form http://www.pharmacy.manchester.ac.uk/bryce/amber  and then replace the AM1-BCC with the resp charge form    http://www.pharmacy.manchester.ac.uk/bryce/amber  . At last, i use "acpype –i ben.mol2 –c user" to get the nad.itp file.
>          so the NAD+ use the RESP charge and the ligand use the   AM1-BCC charges , can i do like this ?
>          i use this method to get the NAD+.itp file? is correct or not ?

Why not just use the parameters that are already published?  Unless there's 
something wrong with them, there's no need to reinvent the wheel.



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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