AMBER Archive (2005)

Subject: Re: AMBER: align snapshots to a reference

From: Wen Li (liw_at_wadsworth.org)
Date: Wed Mar 30 2005 - 09:43:21 CST

Dear Dr. Simmerling,

Thanks for your help. What we want to do is using one snapshot (say a
protein, not include ions and waters) of an MD trajectory as a reference
aligns other snapshots to this reference, and then write out the
coordinates of the aligned snapshots.

I was hoping that you could provide information on which commands of
ptraj should be used.

Thanks,
Wen

On Tue, 29 Mar 2005, Carlos Simmerling wrote:

> ptraj does this- if that's not what you want, you;ll have to be much
> more specific.
>
> Wen Li wrote:
>
> >Hello everyone,
> >
> >I am wondering if there is a program available for a purpose of aligning
> >snapshots along a trajectory to certain residues of a reference
> >structure, and write out the coordinates of all aligned snapshots.
> >
> >Thanks,
> >Wen
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