Also, you'll need to use the topology file that has the same atoms as the
ones remaining in the stripped coordinate file (thus, you need a stripped
topology file for any kind of visualization or future analysis of a stripped
topology file).
If you are still using the original topology file for the stripped
trajectory, you'll get very warped, nonsensical structures. Also make sure
that you're using the correct "with box coordinates" or not (if your
original MDCRD had box coordinates and you didn't explicitly write "nobox"
on the trajout line, you still have the box info).
Another suggestion -- use NetCDF format for all trajectories (printing from
sander/pmemd and dumping from ptraj/cpptraj by putting the "netcdf" word at
the end of the trajout command).
This avoids these problems and has lots and lots of benefits.
HTH,
Jason
On Sun, Oct 16, 2011 at 12:59 PM, David Case <dacase.rci.rutgers.edu> wrote:
>
>
> On Oct 16, 2011, at 12:16 PM, "Ouaray Z." <zo1g10.soton.ac.uk> wrote:
>
> >
> > I am using Amber coordinates option when i load the mdcrd file .
>
> Since you did not use the "nobox" option when makng the stripped trajectory
> file, you need to use the "Amber coordinates with periodic box" option in
> VMD.
>
> > Otherwise i have 2000 frames in the trajectory. but when i download the
> ptraj result file "MD_PC_NoWat_test.mdcrd" i've got 398 frames while i am
> suppose to obtain only 10 frames using "trajin 2AHI_MD1.mdcrd 1 9999999999
> 100".
>
> If you originally have 2000 frames, and ask ptraj to output every 100th
> frame, you should end up with 20 frames. But it is unclear what you are
> *really* doing when you "download the ptraj result file", or what is
> indicating that you have 398 frames. I don't think we can help much without
> knowing more precise information.
>
> ....dac
>
> >
>
> _______________________________________________
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> 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 Mon Oct 17 2011 - 04:30:03 PDT
