Dear Daniel,
Thanks a lot for the tip, it's working! I also tried with DCD format, and
it also worked.
.Jose
On Mon, Mar 28, 2016 at 5:07 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> The Amber ASCII trajectory format is bad for systems with < 3 atoms.
> Use netcdf instead (trajfmt netcdf).
>
> On Mon, Mar 28, 2016 at 2:21 PM, Jose Borreguero <borreguero.gmail.com>
> wrote:
> > Dear amber users,
> >
> > I have used command vector to create a trajectory of the center of
> > mass and a topology file:
> > vector vcm center out peblock_cm.dat .* trajout peblock_cm.crd parmout
> > peblock_cm.parm
> >
> > These are the first lines of trajectory peblock_cm.crd:
> > Cpptraj Generated trajectory
> > 0.000 0.000 0.000 47.840 49.982 47.580
> > 0.000 0.000 0.000 47.852 50.022 47.566
> > 0.000 0.000 0.000 47.861 50.075 47.547
> >
> > After this I use the topology file and read in the trajectory:
> > cpptraj -p peblock_cm.parm
> >>trajin peblock_cm.crd
> > Reading 'peblock_cm.crd' as Amber Trajectory
> > Warning: Box information present in trajectory but lengths are zero.
> > Warning: DISABLING BOX in parm 'peblock_cm.parm'!
> >
> > As you can see, trajin is "thinking" that the trajectory contains Box
> > info, when this is not the case. Half the lines are assume to be box
> > info so I end up reading every other frame.
> >
> > Is there a way to read this trajectory without assuming box info?
> >
> > Best,
> > Jose Borreguero.
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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>
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Received on Mon Mar 28 2016 - 14:30:05 PDT
