[AMBER] residue wise rmsd, not getting expected results

From: vaibhav dixit <vaibhavadixit.gmail.com>
Date: Mon, 12 Jul 2010 14:00:55 +0530

Dear Amber community member,
I have performed 1ns MDS on protein-ligand complexes. Now I'm interested to
know the rmsd residue wise fluctuation for each complex which I can plot
using xmgrace and show that a few ligands stabilizes H-12 helix while others

For this I'm using the following input file for ptraj with the command

$AMBER/exe/ptraj 2PRG_rosi.prmtop < rosi_MD_backboneAF2.in

trajin rosi_MD_equil.mdcrd
trajin rosi_MD_1ns.mdcrd
rms first out rosi_MD_backboneAF2.rms :259-271.N,C,CA
The command runs successfully and generates the file rosi_MD_backboneAF2.rms
(file attached), but when I plot using xmgrace it gives 800 point on the
x-axis instead of AA number i.e. 259 to 271.

Please suggest the necessary modification so that I can actually get the
residue wise rmsd which I can compare for different ligands.
Waiting for your response and help...
Thanks in advance...

With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X,  S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com

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Received on Mon Jul 12 2010 - 02:00:03 PDT
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