AMBER Archive (2004)

Subject: Re: AMBER: Amber7:

From: FyD (
Date: Thu Jun 03 2004 - 15:11:28 CDT


> 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.


Best regards, Francois

F.-Y. Dupradeau
The Scripps Research Institute, San Diego, CA
Faculte de Pharmacie, UPJV, Amiens, France
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