Thanks Jason,
Thats great. I will try that up. Regarding mdcrd file, can you suggest me
how to proceed further. Lets say
I have coordinates for three time points:
ATOM1 ATOM2
x1 y1 z1 X1 Y1 Z1
x2 y2 z2 X1 Y1 Z1
x3 y3 z3 X1 Y1 Z1
On Thu, Feb 28, 2013 at 2:33 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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 - 07:00:02 PST
