On Sat, Mar 16, 2013 at 7:04 AM, . mirage <m.o.m.live.fr> wrote:
>
> Hi,
> Thank's for all reply
>
> My question is to calculate the angle formed between two plan function of
> time of my trajectory with amber
> Thomas suggest the function "black box" of NAB, is there any
> clarification?
>
NAB is a program that has numerous options for molecular modeling and
geometric manipulation. Look through the first NAB chapter in the
AmberTools manual to see if any of the functionality will do what you want.
If not, you will probably have to write a script or program to calculate
the angle between the two planes (which I would probably do by calculating
the angles between the normals of the two planes calculated via the
cross-product of the two vectors making up each angle). I don't think
there is any cpptraj or ptraj command to do exactly what you want.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Mar 16 2013 - 06:00:02 PDT
