AMBER Archive (2000)

Subject: RST file for non-standard residue

From: arubin_at_unmc.edu
Date: Mon Dec 18 2000 - 16:08:40 CST


Dear AMBER users,

I want to carry out MD run for short peptide by the SANDER program ( AMBER
6) with NMR constraints derived from DIANA files.
One of peptide residues is non-standard residue( Threonine linked with
sugar ) which is not described in map.DG-AMBER and tordef.lib files
necessary for using of standard procedures ( makeDIST_RST and make ANG_RST
) to convert a simplified description of distance and angle bounds into
a detailed input ( RST file ) for SANDER.

Thus my question is how to create RST file with description for
non-standard residue?

Alexander Rubinshtein, Ph.D.
UNMC Eppley Cancer Center
Molecular Modeling Core Facility
_________________________________
University of Nebraska Medical Center
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Office: (402) 559-5319
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E-mail: arubin_at_unmc.edu