AMBER Archive (2003)

Subject: AMBER: N/C termini

From: Xavier Periole (periole_at_inka.mssm.edu)
Date: Wed Jul 16 2003 - 17:24:19 CDT

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
 
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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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