AMBER: problems with mdcrd

From: Carsten Detering <>
Date: Thu, 08 Jul 2004 10:16:04 -0700

Hi Ambers,

I want to calculate mm-pbsa on a complex. I have done MD production runs
  on the ligand, the receptor, and the complex, respectively. While I am
able to look at the receptor and the ligand trajectories, I cannot open
the complex mdcrd file in VMD ('unable to load molecule'), and also the
postprocessing with ptraj doesnt work. It gives me the error

PTRAJ: trajin
Checking coordinates:

Could not open file ( with mode (r)
WARNING in checkCoordinates(): Could not open file (
WARNING in ptrajSetupIO(): trajin, cannot open file...

The complex-mdcrd from the heating process I can load alright.
Looking at the three mdcrd files does not reveal any significant
differences to me.

Does anybody have a suggestion what might be causing this problem?

Thanks in advance,


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Received on Thu Jul 08 2004 - 18:53:00 PDT
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