AMBER Archive (2009)

Subject: [AMBER] rms fit of mutant with respect to wild type structure

From: Siddharth Rastogi (
Date: Thu Oct 29 2009 - 08:55:12 CDT

Dear Amber users,
I am interested to get RMS fit of Mutant with respect to wild type
structure. I have used the following input file

reference 1WT.pdb
trajin MUT_prod_1_1ns.mdcrd.gz 1 1 1
strip :WAT
strip :Cl-
center :1-100_at_CA
image center familiar
rms reference out rmsd_WT_MUT :1-100_at_CA

The value obtained from the output file is around 4 Angstroms. But I got
0.8 Angstroms using Chimera for the same two structures. There is some
problem with the above syntax it seems. But I am not getting the problem.
Can anyone help me in this regard.

Siddharth Rastogi
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