AMBER Archive (2004)

Subject: Re: AMBER: Amber7:

From: FyD (fyd_at_u-picardie.fr)
Date: Thu Jun 03 2004 - 15:11:28 CDT

Hi,

> I want to create a polymer structure like polyhydroxyalkanoates
> (PHAs, having around 1000 atoms) in xleap. but I dont know what
> charges I should assign with atoms?

I guess you have a repetitive UNIT in your polymer. Why don't you get the RESP
charges for this unit instead of for all your polymer and create your own OFF
library ?

I think you can apply the startegy followed by Cieplak et al. for peptide and
nucleic acid topology database to your polymer.

See http://structbio.vanderbilt.edu/archives/amber-archive/2004/1561.phtml

Best regards, Francois

F.-Y. Dupradeau
 --
The Scripps Research Institute, San Diego, CA
Faculte de Pharmacie, UPJV, Amiens, France
 --
http://www.u-picardie.fr/labo/lbpd/fyd.htm
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