AMBER Archive (2008)

Subject: Re: AMBER: Is there a way to cluster frames of a trajectory?

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Wed Aug 27 2008 - 19:56:08 CDT

ptraj can do this

Sasha Buzko wrote:
> Hi all,
> could you possibly suggest an existing piece of software to run
> clustering of frames in a trajectory (by mutual RMSD). We are trying to
> get an estimate of which conformations of a protein are prevalent and
> how much time the protein spends in each conformational group (within
> some rmsd tolerance).
>
> Thanks for any hints
>
> Sasha
>
>
> Urszula Uciechowska wrote:
>> Dear Amber users,
>>
>> I am trying to use ptraj (amber 9) to analysis LES trajectoreis but I
>> am getting only one traj file (I made 5 copies) I appreciate very much
>> if somebody could tell me how to do this properly with ptraj or maybe
>> there are other possibilities?
>> thanks in advance Urszula
>>
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> 

-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
                             Quantum Theory Project
                            Department of Chemistry

                  Senior Editor. Journal of Physical Chemistry
                           American Chemical Society

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu
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