Re:Re: [AMBER] remove water from system

From: Yunfen Wang <>
Date: Wed, 21 Apr 2010 08:53:36 +0800 (CST)

Thank you very much, Jason.


2010-04-20 20:16:42"Jason Swails" <> д
>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

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Received on Tue Apr 20 2010 - 18:00:03 PDT
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