Subject: calculate rmsd from two pdb files in CHARMM

From: Alice NgarKit Ko <[email-masked]>
Date: Tue, 8 Oct 2002 12:25:27 -0500 (EST)

Hi,

I have two pdb files.  I want to find the rmsd of 3 of the atoms.  
Can someone tell me how to do that?  Thanks

Alice

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From: Rick Venable <[email-masked]>
Date: Tue, 8 Oct 2002 13:50:50 -0400

> Can someone tell me how to do that?  Thanks

The short answer is to put the 2nd set of coords in the COMP coord set,
and then use the COOR ORIENT RMS command with the appropriate atom
selection for the 3 atoms.

If the PDB files are for the same protein and can be read independently
via the same PSF, the above is about all that's needed; just use the
COMP keyword when reading the 2nd file.

For non-identical proteins, the procedure is a bit more complicated.  
You must create a PSF which encompasses both proteins, and read both
sets of coords into the MAIN (default) coord set.  Then use COOR COPY
COMP to put all coords in the comparison coord set as well.  Finally,
use COOR DUPL to copy selected atomic coords from one protein to another
within the COMP set.  Then you can again use COOR ORIENT RMS to compute
RMSD for the selected atoms. 

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Rick Venable           29/500
FDA/CBER/OVRR Biophysics Lab
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Rockville, MD  20852-1448  U.S.A.
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From: Michael Crowley <[email-masked]>
Date: Tue, 8 Oct 2002 12:21:18 -0700

Apologies to Alice, I missed the title that you were using charmm.
I had suggested that the easiest way for 3 atoms was to do it
by hand. However if you have charmm already set up for this system,
then Rick's suggestion is definitely the easiest.
Mike

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