AMBER Archive (2005)

Subject: RE: AMBER: Coordinate Superimposition in PTRAJ

From: Vineet Pande (pande_vineet_at_hotmail.com)
Date: Mon Jan 17 2005 - 03:45:20 CST


Thanks Dr. Ross:
>
>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.
>
Does VMD also write an output with all the atoms superimposed/ transformed
coordinates and with the same names as input file, esp. for hydrogens?
Though I have to try using the latest version of VMD you mentioned..
Cheers,
Vineet

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