On Mar 16, 2013, at 7:34 AM, Jason Swails wrote:
> 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
>
Well, I did not remember exactly correctly, but on pages 390-391 of the
AmberTools manual (version 12) are described the functions torsion()
and torsionp(). torsion() calculates the torsional angle between four
atom expressions (read the nab documentation for the definition of these)
and torsionp() gives the torsional angle between 4 explicit points in
Cartesion 3-space. Also, the function plane() calculates the least
squares plane between four atom expressions in the form z = Ax + By + C,
and that function might be useful in other aspects of your analysis.
But Thomas's suggestion about the arccos of the dot product of the two
plane normals is the correct math answer to your question. No nab
program is required, although your specific application seems like a
good place to use nab. Any good book on analytic geometry (at least
that is what it was called when I was an undergrad) can provide the
answer to your question as posed or any of the Google search hits I
suggested will do so as well. Feel free to ask questions about using
nab here, but please read the documentation first.
My point was that questions about math, even if the question arises in
the context of molecular biophysics, are better posed in a forum devoted
to math, not AMBER. You complained that no one had answered your
question after 24 hours. I suggest that is because you asked it in the
wrong place. That is all I meant.
HTH,
Bud Dodson
PS, I did not look at the source code, but I am confident that the nab
torsion functions work exactly as Jason described.
--
M. L. Dodson
Business email: activesitedynamics-at-gmail-dot-com
Personal email: mldodson-at-comcast-dot-net
Gmail: mlesterdodson-at-gmail-dot-com
Phone: eight_three_two-five_63-386_one
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Received on Sat Mar 16 2013 - 07:00:03 PDT
