RMSD by residue (fwd)

From: <amber_at_heimdal.compchem.ucsf.edu>
Date: Mon 26 Aug 2002 14:49:39 -0700 (PDT)

---------- Forwarded message ----------
Date: Tue, 20 Aug 2002 19:21:42 -0400
From: Jianhui Wu <wujih_at_BRI.NRC.CA>
To: amber_at_heimdal.compchem.ucsf.edu
Subject: RMSD by residue

Dear Amber users,

Using ptraj, I try to calculate the RMSD by residue between two
average structures of the same complex (pdb files). The following script
only give me the overall RMSD. Is there any way to modify it to output the
RMSD by residue? If not, could you point me to the suitable module in

I know that "rms reference mass out rms_res1.dat :1_at_CA,C,N" will give me
the RMSD for residue 1. But I would be surprised if I have to do it for
every residue in this way.

#!/bin/csh -f
${AMBEREXE}/ptraj ../../test.top << End
trajin ./test_avg1.pdb
reference ./test_avg2.crd
center :1-260 mass origin
rms reference mass out tst_rms_BB_1-260.dat .CA,C,N
rms reference mass out rms_res1.dat :1_at_CA,C,N



Thanks a lot,

Jian Hui
Received on Mon Aug 26 2002 - 14:49:39 PDT
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