Re: vmd-l: conformational alignment

From: John Stone (
Date: Wed Mar 30 2005 - 15:30:26 CST

  You might want to check out Luis Gracia's "RMSDTT" plugin for VMD,
as I believe it would do the alignment for you without much effort:

Once aligned, it is easy to write out the new coordinates using
'mol writeXXX' and such.

  John Stone

On Wed, Mar 30, 2005 at 04:21:26PM -0500, Wen Li wrote:
> Hello everyone,
> I hope that you could help me on the following question with either vmd
> or namd, or any program:
> I have an MD trajectory generated using AMBER, and I want to align
> snapshots of this trajectory to the coordinates of a reference structure.
> And then write out the coordinates of each aligned snapshots. Is this
> doable in VMD?
> Thanks,
> Wen

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