Depending on how you define the domains and their mutual rotation,
ptraj's angle, dihedral or vector commands might do it for you. If
the domains pivot around a common point, you could define three
centers of mass using appropriate sets of atoms and get the angle.
There are analogous procedures for dihedral and vector.
On Tue, May 18, 2010 at 2:30 AM, Tan Yaw Sing <tanys.bii.a-star.edu.sg> wrote:
> Hi Amber users,
>
> I have a trajectory of a protein with two domains and I am trying to
> characterise its interdomain motions. I would like to obtain the angle of
> rotation between the two domains during the course of the trajectory. Is
> there a way to perform this kind of analysis in ptraj? Thank you for your
> help.
>
> Regards,
> Yaw Sing
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>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Tue May 18 2010 - 13:30:04 PDT
