Re: conformational alignment

From: Giovanni Bellesia (
Date: Wed Mar 30 2005 - 16:40:36 CST

Hi Wen,
the simplest thing to do is probably to take a look at the vmd user's
- node 121; Tcl text command "measure fit"
- node 181: RMS and alignment
you will find clear instruction there, together with a few short useful
example scripts.


On 30 Mar 2005, at 22:21, 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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