AMBER Archive (2005)

Subject: Re: AMBER: Neutral C-terminal residue

From: FyD (fyd_at_u-picardie.fr)
Date: Wed Oct 19 2005 - 07:17:12 CDT

Quoting Sébastien Fiorucci <Sebastien.fiorucci_at_unice.fr>:

> I need to perform a simulation with a neutral isoleucine c-terminal
> residue. Only COO- parameters are avalaible in the Amber Force Field.
> Does anyone know where can I found parameters for neutral C-terminal
> residue?

You could follow what has been done by:
P. Cieplak, W.D. Cornell, C.I. Bayly & P.A. Kollman J. Comput. Chem. 1995, 16,
1357-1377.
See also the RED FAQ http://www.u-picardie.fr/labo/lbpd/RED/FAQ-I.htm

You could also use CH3CO-NHCHRCOOH and get the RESP charges using
intra-molecular restraints for CH3CO = 0.

This is automatically done in R.E.D.-III. We hope to release it sometime
beginning of next year...

regards, Francois

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