[Dock-fans] The charge about cofactor

Scott Brozell sbrozell at rci.rutgers.edu
Tue Sep 24 20:03:15 PDT 2013


Hi,

On Tue, Sep 24, 2013 at 03:56:28PM +0800, aixintiankong wrote:
>      In my system, The active site of protein have a cofactor NAD+, and the NAD+ interact with the ligand. so i must keep the cofactor. but when i use chimera to add Am1-BBC orgasteiger the charge of  atom  N1N is negative, but in fact the N1N should be positive charge. so, i don't  know how to deal with the charge of NAD+ in docking. please help me !
>     i think i can get the resp charge of the NAD+ frome http://www.pharmacy.manchester.ac.uk/bryce/amber for the NAD+. but i don't could i use the charge of  Amber ff12 for protein, resp charge for the cofactor and the gasteiger charge for the ligands (i want to do virtual screeing )?  the methods is right or worng? please give me some advice. thank you very much!

Have you investigated why Chimera produces a negative charge on N1N ?
This may be a symptom of other problems, e.g., a poor geometry.

Yes there are contributed parameters with a positive charge on N1N:
http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/cof/NAD+.lib
 "N6" "NF" 0 1 131072 36 7 0.097406

Since some parts of the system may be more charge model sensitive than others,
it seems reasonable to mix charge models.  You can search the literature for
common practice in virtual screening.

I do not understand your mention of Amber ff12; this is not used by DOCK.  See
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#vdwdefn
and the files:
dock6/parameters/vdw*

scott


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