AMBER Archive (2005)

Subject: Re: AMBER: capping

From: FyD (fyd_at_u-picardie.fr)
Date: Wed Apr 27 2005 - 11:40:36 CDT

> I am doing simulation of free amino acid as a ligand in protein. I would
> like to cap the amino acid at N and C terminal. Even leap doesnt include
> missing hydrogen atom at the N terminal.Give me some suggestion how to
> perform capping in amber. I am a new amber user. Any suggestion is
> appreciated.

- Read this paper:
Cieplak et al. J. Comput. Chem 1995, 16, 1357-1377

- See http://www.u-picardie.fr/labo/lbpd/RED/
and the corresponding FAQ
http://www.u-picardie.fr/labo/lbpd/RED/FAQ-I.htm

- Also use http://amber.scripps.edu/
and do a Google search in mailing list archives

Regards, Francois

  F.-Y. Dupradeau
DMAG EA 3901 & Faculte de Pharmacie, Amiens, France
The Scripps Research Institute, La Jolla, CA, USA
       --
http://www.u-picardie.fr/labo/lbpd/FyD.htm
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