AMBER Archive (2004)

Subject: AMBER: leap - orientation of sequenced residues

From: Sarah Wittkopp (tschampe_at_sunchem.chem.uga.edu)
Date: Mon Feb 02 2004 - 19:58:33 CST

Hi,

I am trying to determine where in the leap source code the orientation
between residues that are joined/sequenced together is specified - based
on the prep files.

For example, if I used the command in leap " peptide = seq { ALA ALA } "
where in the source code would it define how to orient these two residues?

It was clear in the old prep, edit, link style that it was explicitly
based on overlaying of the dummy atoms with the main chain atoms of the
previous residue, but I have not explicitly found this in the leap code.

If anyone is familiar with this I would be very grateful for some help.

-Sarah

_________________________________
    
Sarah Tschampel Wittkopp
Woods' Research Group
Complex Carbohydrate
Research Center
University of Georgia
315 Riverbend Road
Athens, GA 30602-4712
OFFICE: (706) 542-0263
_________________________________

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