Subject: CCL:AMBER7/Cyclic Peptide

From: Gitanjali Yadav <[email-masked]>
Date: Fri, 02 May 2003 16:51:46 +0530 (IST)

hi all
How can one make required input files for simulation of a
cyclic peptide in AMBER7. What I have is a starting coordinate
for this peptide in PDB format.

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From: "David A. Case" <[email-masked]>
Date: Fri, 2 May 2003 08:21:22 -0700

> for this peptide in PDB format.

See the instructions for LEaP, Chapter 5 of the Users' Manual.  Basically,
after loading the force field you want, you use the "loadPdb" command to
read in the coordinates and sequence from the PDB file.

There are detailed tutorials available at the Amber web site,

    http://www.amber.ucsf.edu/amber/

The best place to ask Amber-related questions is the Amber reflector:

    [email-masked]

(more info about this is on the web site, above).

..good luck...dac

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