AMBER: N/C termini

From: Xavier Periole <>
Date: Wed, 16 Jul 2003 18:24:19 -0400

Hi Luis and others,

thanks for your comment. If I got Amber right the alln(or c).in contains
the N(or C)-terminus with the NH3+(or COO-) attached to all the
residue types and their are refered by the N(or C)-residue type:
NVAL (or CVAL) for example. That is the more common way to
do. After it seems that you can use the "protecting" residues (ACE/NME)
that give a neutral N(or C)-terminus, and you add them by adding the
residues ACE or NME in your sequence.

I want something different and idealy simplier. I want to neutralize the
termini by only adding a Hydrogen on the N-terminus Nitrogen or on
a C-terminus Oxigen. And that I did not find in the topology files.

I was wandering if somebody had generated the topology of those
termini. They are pretty common.

Thanks for your time

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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Received on Wed Jul 16 2003 - 23:53:01 PDT
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