AMBER Archive (2008)

Subject: AMBER: VMD file generation 4 - mdcrd ptraj analysis

From: Campbell, Patrick (
Date: Mon Jun 02 2008 - 13:26:15 CDT

Hello All,
Following on the advice of Drs. Ross and Ibrahim, I ran a trajin analysis in ptraj to check the mdcrd file of my MD output ( I was getting difficulty generating slides for viewing in VMD - instead of a few thousand, I was only getting 12 slides from a 10 ns MD run).
The following error messages came up with the analysis

Error scanning a value: pert, ictper

Error scanning a value: pert, icpper
  Extra perturbation information...
Error scanning a value: pert, iacper
Successfully completed readParm.
Initializing state: detected PBC beta angle in prmtop that is not 90.0!
PTRAJ: Processing input file...
       Input is from standard input
It would appear that there are some errors with the mdcrd file.
I would appreciate any suggestions as to how I should proceed from this point. Ultimately, I would like to have a fully generated movie from the mdcrd file.
Thanks again for all your hellp and do have a great day!

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