[AMBER] cpptraj: Per residue rmsd

From: George Tzotzos <gtzotzos.me.com>
Date: Sat, 02 May 2015 20:37:51 +0200

Im trying to work out the average rmsd over time of each residue in a protein receptor.

The script Im using is the following:

parm 4fqt_OVT_solv.prmtop [MD]
parm 4fqt_new.pdb [Xray]
trajin prod_0-20ns.nc [MD]
reference 4fqt_new.pdb parm 4fqt_new.pdb [4FQ]

rmsd :10-125 reference perres perrescenter perresout PRMS.dat range 10-125 perresmask &!.H,N,CA,HA,C,O
run
xmgrace PRMS.dat

I assume it is not correct as the output produced (see snapshot below) is not the expected one. In the x-axis instead of residue number, I get frame number.

Id appreciate any suggestions in correcting the above script.

Regards

George


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Received on Sat May 02 2015 - 12:00:03 PDT
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