On Thu, Feb 28, 2013 at 7:00 AM, HM <scienceamber.gmail.com> wrote:
> Hi All,
> I extracted the Center of mass of two domains. Now I want to visualize
> these coordinates in VMD. For the same, I plan to make a new parameter and
> coordinate files.
>
> I am planning to do something line
>
> prmtop file: only two atoms (say two C atom)
>
> mdcrd file : coordinates of these two atoms in different time point.
>
> I was just wondering if it is possible to make files with these
> information..
>
Sure. The easiest way might be to use ParmEd to strip all atoms except the
oxygen atoms from 2 water molecules from one of your topology files (since
all you need is a topology file with 2 atoms). As another thought you
could generate a prmtop in tleap with only 2 sodium ions.
The mdcrd you will probably have to generate using your own script, since
no program in Amber will do what you want, I don't think.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Feb 28 2013 - 06:00:03 PST
