you want to use a combination of "reference" "rms" and "trajout".
that should do it. the DNA tutorial on the amber web page shows
how to use the reference and rms commands, and trajout is pretty
easy to follow in the amber manual.
you might use something like this:
trajin ./md.x
trajout ./md.fit.x
reference ./ref.crd
rms reference out rmsd.dat .CA,C,N,O,H
go
Wen Li wrote:
>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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Received on Wed Mar 30 2005 - 17:53:00 PST
