[Dock-fans] Dock-fans Digest, Vol 112, Issue 6

aixintiankong aixintiankong at 126.com
Wed Sep 25 18:28:54 PDT 2013


only hi ?








At 2013-09-26 03:00:02,dock-fans-request at docking.org wrote:
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>Today's Topics:
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>   1. Re: The charge about cofactor (Scott Brozell)
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>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Tue, 24 Sep 2013 23:03:15 -0400
>From: Scott Brozell <sbrozell at rci.rutgers.edu>
>Subject: Re: [Dock-fans] The charge about cofactor
>To: aixintiankong <aixintiankong at 126.com>
>Cc: dock-fans at docking.org
>Message-ID: <20130925030315.GM30380 at casegroup.rutgers.edu>
>Content-Type: text/plain; charset=utf-8
>
>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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>End of Dock-fans Digest, Vol 112, Issue 6
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