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[Molecular-modelling] Re: Molmodel Digest, Vol 20, Issue 3

Sunil Patel via molmodel%40net.bio.net (by sunil.patel from camcellnet.com)
Mon Jun 2 07:13:58 EST 2008


Hi Vladimir ,

The problem with docking inorganic molecules into protein structures is with
at atom typing ie Charges to be placed on the atoms..fully charged, partial
charges. Most forcefields are either biased to proteins or inorganic
molecules and metals. There is no comprehensive forcefield that covers all.
You will need to check the forcefield library for the atoms and molecules
covered. In general people approximate the charges. Run the expts, see if
the molecule is distorted. Rerun expts to overcome after charge
modifications for adjusting the distortions.

regards,

Sunil.



On 31/05/2008, molmodel-request from oat.bio.indiana.edu <
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>   1. Re: inorganic mol. docking (Vladimir Petrov)
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> Date: Fri, 30 May 2008 18:16:04 -0400
> From: Vladimir Petrov <vpetrov from sco.com>
> Subject: [Molecular-modelling] Re: inorganic mol. docking
> To: molmodel from net.bio.net
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> sudha.mrig from gmail.com wrote:
> > I want to dock an inorganic molecule like ZnSO4, MgOAc etc. with a
> > protein molecule.
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> I guess, you'd have to familiarize yourself with basics of General
> Chemistry first, and then decide how to dock ZnSO4 "in organic molecule"
> into the protein structure...
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