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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Received on Mon Mar 28 2016 - 13:30:03 PDT
