When I've tried to convert my amber 100ns trajectory to dxd using cpptraj
it took about 1 hour :) Does catDCD or any other terminal utilities can do
such tasks?
By the way also I have a question about proper loading of the trajectories
to the VMD
e.g using
vmd ionized.prmtop md.mdcrd
VMD recognize this trajectory as without PB box. Does it possible to fix it
providing some flag to VMD?
James
2014-05-21 19:38 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
> On Wed, 2014-05-21 at 19:19 +0400, James Starlight wrote:
> > Thanks Dan!
> >
> > Could someone suggest me some unix utility useful for the conversion of
> the
> > amber's trajectory format to the charm-like .dcd ?
>
> cpptraj also does that. If you name the trajectory something ending in
> ".dcd" in the trajout command, cpptraj will output a CHARMM-like DCD
> file. You can also use the keyword "dcd" to force cpptraj to write a
> DCD file.
>
> I think it may be beneficial to spend a few minutes with the manual and
> try to answer some of your own questions (through reading the relevant
> parts of the manual and trial/error) rather than asking everything here.
> You can also often Google your questions and get helpful hits on the
> first page. This would probably save you (and us) time.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
> _______________________________________________
> 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
Received on Thu May 22 2014 - 06:00:04 PDT
