2010/4/21 Yunfen Wang <wangfen041237.163.com>
>
>
>
> Thank you very much , Jason!
>
> as you say " I know that VMD makes it quite easy to measure dihedrals,
> distances, or angles and
> plot them as a function of time.“
>
> But I did not find the tool in VMD menu for measuring dihedrals,
> distances, or angles and
> plot them as a function of time.Could you explain it for me ?
>
On the main menu, go to Mouse->Label. This will open up a menu that will
allow you to label a single atom (you can also access this by pressing the
number '1'), a distance (accessed by pressing '2'), an angle (by '3'), and a
dihedral angle (by '4'). Then select any 1, 2, 3, or 4 atoms you want
(based on what you're trying to measure), to measure that value.
The location Carlos suggested will show you the value of the item you chose
to measure (and also allow you to plot it versus time/frame).
Good luck!
Jason
>
>
>
> Thanks a lot !
>
> Wang
>
>
> 在2010-04-20 20:16:42，"Jason Swails" <jason.swails.gmail.com> 写道：
> >Hello,
> >
> >If you are trying to measure a particular dihedral angle as the simulation
> >progresses, you can do this with ptraj using the "dihedral" command, which
> >is clearly explained in the manual.
> >
> >Alternatives are to use molecular visualization programs, such as pymol
> and
> >VMD. I do not use pymol regularly, though I believe it can do this. I
> know
> >that VMD makes it quite easy to measure dihedrals, distances, or angles
> and
> >plot them as a function of time. If you are looking for the value of the
> >dihedral as a function of time, you do not just need the trajectory of the
> >Pr only (whatever Pr may be...). However, if you only want the Pr part,
> use
> >the strip command like Carlos suggested (which is also detailed quite
> >thoroughly in the manual). Note that if you keep it as an mdcrd or netcdf
> >file, you'll have to create a matching prmtop to make use of it.
> >
> >Good luck!
> >Jason
> >
> >On Tue, Apr 20, 2010 at 4:09 AM, Yunfen Wang <wangfen041237.163.com>
> wrote:
> >
> >> Hi all,
> >> I have done MD simulations of protein in water and got the trajectory
> file
> >> . But now , i want to analysis dihedral angel of the Pr , how can i get
> the
> >> trajectory file of pr only . Or , it just need the final structure of pr
> to
> >> analysis dihedral angel. if this is true , how to character the change
> with
> >> time? Any instruction ?
> >> Thank you !
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> >
> >
> >
> >--
> >---------------------------------------
> >Jason M. Swails
> >Quantum Theory Project,
> >University of Florida
> >Ph.D. Graduate Student
> >352-392-4032
> >_______________________________________________
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> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
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>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Apr 21 2010 - 05:00:02 PDT
