AMBER Archive (2005)

Subject: RE: AMBER: Coordinate Superimposition in PTRAJ

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sun Jan 16 2005 - 12:59:48 CST


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 (http://www.ks.uiuc.edu/Research/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
Ross

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|\oss Walker

| Department of Molecular Biology TPC15 |
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