Re: RMSD by residue (fwd)

From: Holger Gohlke <>
Date: Mon 26 Aug 2002 18:08:35 -0700


> 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
> Amber7?

You might have a look in carnal. In the OUTPUT section, it says for the
TABLE command: "RMS ids default to the rms of the group, while
rmsid%residues ... give per-residue rmsd's".

> 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 ../../ << 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
> go
> End
> exit
> ----------------------------------------------------------------------

Best regards


Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
Received on Mon Aug 26 2002 - 18:08:35 PDT
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