The mdcrd format is 10F8.3 -- meaning 10 numbers in the format XXXX.XXX
(for a total of 80 characters). Any leading X's that are not specified
(because the number is larger than -100 or smaller than 1000) is just
filled with spaces. Then it's xyz1 xyz2 xyz3 ... etc. So something like
this:
x1 y1 z1 X1 Y1 Z1
x2 y2 z2 X2 Y2 Z2
x3 y3 z3 X3 Y3 Z3
Note that you never go out to 10 numbers because each frame has only 6.
Frames are separated by a newline. Be sure that the coordinates are in
the format I described above.
Good luck,
Jason
On Thu, Feb 28, 2013 at 9:29 AM, HM <scienceamber.gmail.com> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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 - 07:30:03 PST
