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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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