From: John Stone (johns_at_ks.uiuc.edu)
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.
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?
-- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns_at_ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
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