the moil-view program calculates RMSD by residue
for amber trajectories.
http://comp.chem.sunysb.edu/mlv.html
----- Original Message -----
From: <amber_at_heimdal.compchem.ucsf.edu>
To: <amber-mail_at_heimdal.compchem.ucsf.edu>
Sent: Monday, August 26, 2002 5:49 PM
Subject: RMSD by residue (fwd)
>
>
> ---------- 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
> Amber7?
>
> 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
> ----------------------------------------------------------------------
>
>
> Thanks a lot,
>
>
> Jian Hui
>
>
Received on Mon Aug 26 2002 - 18:10:41 PDT
