Many thanks Daniel
On Fri, Jan 15, 2016 at 11:58 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
> >> > _______________________________________________
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> >> > 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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Jan 15 2016 - 12:30:03 PST
