RE: AMBER: Saving RMSD values in VMD

From: Ross Walker <>
Date: Fri, 26 May 2006 08:27:08 -0700

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
> please.

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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