[AMBER] cpptraj -- doesn't like reading Amber restart files with more than 99, 999 atoms

From: Ben Roberts <ben.roberts.geek.nz>
Date: Fri, 23 Dec 2011 11:25:29 -0500


I just tried running a wrap command using cpptraj, on an Amber ASCII restart file. The restart file in question contains 311,677 atoms, and is declared to contain such in its header. However, when I tried the trajin command, I got this response:

INPUT: Reading Input from file wrap_and_centre.ptraj
  [trajin BPR-20111213-001_out.rst7]
Error: AmberRestart::SetupRead(): Number of atoms in restart (31167)
       does not match number of atoms in parmtop (311677)
ERROR: Setting up BPR-20111213-001_out.rst7 for read.

The restart file header looks like this:

<start of file>
311677 0.1000000E+03
  28.3626573 14.0009538 -28.1877328 27.4850731 14.2777715 -28.6040488

Now, it appears as though the parsing of the restart file may not cope with more than five characters in the "number of atoms" field. Is this the case? If so, has it been fixed or patched in AT 1.5, or for that matter in the version under development?

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Received on Fri Dec 23 2011 - 08:30:03 PST
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