AMBER Archive (2003)

Subject: AMBER: neutral N- and C- termini !

From: Xavier Periole (periole_at_sci.ccny.cuny.edu)
Date: Wed Jul 16 2003 - 13:52:29 CDT

Hello,

I am going to use Gaussian to make QM/MM calculations where
I'd like to use the AMBER force field for the MM part.
The system I am interested in is a fragment of a protein for which
I want uncharged N-termini (attached to an Arginine) and C-
(attached to a Valine). I have been looking in the topology file of
the C- and N-termini in the dat/leap/prep directory of the force field
(downloaded from the Amber web site) and did not find any sign of
C- and N-termini uncharged: -COOH and -NH2 respectively

Does anybody know if they actually exist somewhere in the topology
files or if there is a common way people treat them in Amber simulations ?

Thanks for your time

Xavier Periole

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Xavier Periole, Ph.D.
Chemistry Dept.
City College of New York (CUNY)
138th St. and Couvent Av.
New York, NY 10010
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