RE: AMBER: Coordinate Superimposition in PTRAJ

From: Ross Walker <>
Date: Sun, 16 Jan 2005 10:59:48 -0800

Hi Vineet,

> I want to superimpose a number of 'different' complexes of the 'same
> protein' with different ligands obtained after a PME/PBC MD
> protocol, and

The latest version of VMD ( can do an
RMS fit of different structures. This can also read amber format files. You
can, for example, load several structures and superimpose them all by RMS
fitting specific atoms. E.g. Alpha-Carbons.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 |
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| | PGP Key available on request |

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Received on Sun Jan 16 2005 - 19:53:00 PST
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