Re: AMBER: Saving RMSD values in VMD

From: Carlos Simmerling <>
Date: Fri, 26 May 2006 11:45:17 -0400

vmd 1.8.4 now has the RMSD trajectory toolkit built in,
it's slightly better at this (and much better for aligning all
frames to view the dynamics). for older vmd you can
download this from the web.

I agree with Ross that getting rmsd data from ptraj is probably the
better way to go for datya analysis.

Ross Walker wrote:

>Hi Nagaraju,
>> I loaded ligand pdb files (same ligand in
>>different conformations) in VMD and calculated RMSD by
>>taking one ligand as reference. Here my question is
>>how to save RMSD values in a file, i have more than
>>two hundred molecules, to note down all values
>>manually is labourious process. Could any body help me
>VMD is not ideally suited to this type of calculation. The RMSD tool is
>really designed to allow you to overlay single molecules to compare the
>differences visually.
>You would be much better using ptraj for what you want to do. You could
>script a ptraj input file to read all 200 structures, measure the RMSD's to
>a fixed structure and then output the whole lot in the form of a table.
>See chapter 10 of the Amber 9 manual.
>All the best
>|\oss Walker
>| HPC Consultant and Staff Scientist |
>| San Diego Supercomputer Center |
>| Tel: +1 858 822 0854 | EMail:- |
>| | PGP Key available on request |
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Received on Fri May 26 2006 - 21:05:26 PDT
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