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.
>
> _______________________________________________
> AMBER mailing list
> 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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 28 2016 - 14:30:03 PDT
