AMBER Archive (2009)

Subject: [AMBER] ptraj image in non-orthorhombic cell

From: Joanna Panecka (panecka_at_icm.edu.pl)
Date: Wed Jun 03 2009 - 15:19:52 CDT

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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