RMSD calculation

From: <arubin_at_unmc.edu>
Date: Tue 15 May 2001 12:43:46 -0700

Dear AMBER users,

I have the AMBER6 trajectory file for 15 residues peptide in water after MD
run. There is correspondent parm file for this system.
I wanted to calculate the RMSD for all structures collected in the
trajectory file with a fragment of the peptide structure (9 residues) with
different parm file. How to do it in CARNAL or any other analysis program
compatible to AMBER6?

Thank you in advance.

Alexander Rubinshtein, Ph.D.
UNMC Eppley Cancer Center
Molecular Modeling Core Facility
University of Nebraska Medical Center
986805 Nebraska Medical Center
Omaha, Nebraska 68198-6805
Office: (402) 559-5319
Fax: (402) 559-4651
E-mail: arubin_at_unmc.edu
WWW: http://www.unmc.edu/Eppley
Received on Tue May 15 2001 - 12:43:46 PDT
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