Interesting - I hadn't considered that someone would want to do this
(pop it on to the to-do list). Right now the vectormath command needs
both data sets to be the same size. You can get around this by
calculating the vector you want fixed, then replicating the data N
times, then read that dataset in with 'readdata' and then proceed as
normal. Your best bet is to put the vector data in a whitespace
delimited file with format e.g.:
#Frame v7
1 -0.1061 -0.5897 -0.8006 2.7365 -3.4377 -10.4497
2 -0.1061 -0.5897 -0.8006 2.7365 -3.4377 -10.4497
...
and make sure you use the 'vector' keyword with readdata so cpptraj
knows it should read as a vector.
Hope this helps,
-Dan
On Fri, Jan 15, 2016 at 10:24 AM, anu chandra <anu80125.gmail.com> wrote:
> Hi Daniel,
>
> Many thanks for your prompt reply. I just have a quick query here. In my
> case, <mask1> in ' vector V1 corrplane <mask1> ' comes from the starting
> structure of simulation and <mask2> in ' vector V2 corrplane <mask2> '
> comes from each frame of the simulation trajectory. This means, every time
> when the 'dotangle' is calculated the V1 remains constant (as the vector
> comes from starting structure) and V2 get update from frame to frame. I
> just wonder whether this can be possible with the steps you suggested.
>
> Many thanks once again
>
> Anu
>
> On Fri, Jan 15, 2016 at 3:59 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi,
>>
>> You could probably do what you want with 2 'vector corrplane' commands
>> to get vectors normal to the planes defined by whatever atoms you
>> want, then 'vectormath dotangle' to get the angle between them.
>> Something like:
>>
>> vector V1 corrplane <mask1>
>> vector V2 corrplane <mask2>
>> vectormath vec1 V1 vec2 V2 dotangle out angleV1V2.dat
>>
>> Hope this helps,
>>
>> -Dan
>>
>> On Fri, Jan 15, 2016 at 5:58 AM, anu chandra <anu80125.gmail.com> wrote:
>> > Dear Amber users,
>> >
>> > The protein I am working with have three domains. Now I am trying to
>> > calculate a dihedral angle defined by two structures, the starting
>> > structure and a snapshot from simulation trajectory. More precisely, a
>> > plane is drawn between the center of mass of three domains, and the
>> > dihedral angle of interest is formed by this plane from starting
>> structure
>> > and a simulation snapshot. I just wondering possibilities of doing such
>> an
>> > angle calculation with CPPTRAJ.
>> >
>> >
>> > Any help is appreciated
>> >
>> > Anu
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
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Received on Fri Jan 15 2016 - 10:30:03 PST
