Dear AMBER Users,
I performed MD simulation in NAMD using AMBER forcefield, in PBC with
truncated octahedron cell. Then I tried to analyze trajectories with
ptraj, but unfortunately IMAGE command didn't work.
I searched through AMBER mailing list archives, but I haven't found
the solution.
My PTRAJ input:
trajin ../traj_prod.dcd 1 5000 10
# origin at the oligomer
center :1-10 mass origin
image origin center familiar
strip :WAT
trajout ../test_center_nowat.dcd charmm
The system was centered properly, but IMAGE command gave no effect. I
tried also many more variations of the command apart from that version
above, but none worked.
I would be very grateful for any suggestions how could be the reason
for the problem.
Joanna
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Received on Thu Jun 04 2009 - 01:12:52 PDT
