AMBER Archive (2002)

Subject: Re: RMSD by residue (fwd)

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Mon Aug 26 2002 - 20:08:35 CDT

Hi,

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

Best regards

Holger 

-- 
+++++++++++++++++++++++++++++++++++++++++++++
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
email: gohlke_at_scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++