AMBER Archive (2006)

Subject: AMBER: ptraj: nofit option for rmsd

From: Joseph Nachman (nachman_at_hera.med.utoronto.ca)
Date: Tue Aug 08 2006 - 10:27:41 CDT

Hello Amberites:

I'm doing MD simulations on a protein-peptide complex using Amber6. Since
I'm intersted only in the peptide, I keep the protein fixed (using
ibelly).

I'm trying th calculate the rmsds of the peptide, and since the protein is
fixed, I use the option "nofit" to calculate the rmsd. I initially
calculated rmsds without the nofit option (since the frames are lready
fitted to each other, by virtue of the much larger protein being kept
fixed during the simulation), but it appeared that ptraj fitted the mask
(I used first only 10 frames, and by visual inspection I noticed that the
results didn't make sense); I then repeated the calcutaion using the
"nofit" option, but theresults were I identical to those obtainede without
using "nofit".

If I calculate the rmsds for the entire system (protein_peptide) the
results are correct, but I'm intersted only in the peptide. Any ideas?
Thanks,

Joseph

Here is my ptraj input file:

trajin /disk2/nachman/1spsan/5000/1-10.crd
rms first out 1-10.rms_nofit :104-111_at_CA nofit 

-- 
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Joseph Nachman				Department of Biochemistry
nachman_at_hera.med.utoronto.ca		University of Toronto
					Medical Sciences Building
tel: +1 416 978-0560			Toronto, Ontario M5S 1A8
fax: +1 416 978-8548			Canada
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