AMBER Archive (2005)

Subject: Re: AMBER: align snapshots to a reference

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Wed Mar 30 2005 - 10:28:13 CST

it looks ok to me, does it work?
you'll need a prmtop with no water/cl/na to be able to
look at or analyze the trajectory that you write (since you use the
strip commands)

===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

Wen Li wrote:

>Dear Dr. Simmerling,
>
>I was hoping that you could make comments on if the following works for
>the procedure that I described earlier:
>
>trajin MDtraj1 1 1000 100 (one snapshot from each 100)
>reference my_reference_snap (a reference snapshot)
>trajout aligned_traj (includes 1000/100 = 10 snapshots)
>rms my_reference_snap out rms @P (for an RNA molecule)
>strip :WAT
>strip :Cl-
>strip :Na+
>go
>
>
>On Wed, 30 Mar 2005, 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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