Re: [AMBER] remove water from system

From: Jason Swails <>
Date: Tue, 20 Apr 2010 08:16:42 -0400


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!

On Tue, Apr 20, 2010 at 4:09 AM, Yunfen Wang <> 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 !
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Tue Apr 20 2010 - 05:30:02 PDT
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