[AMBER] Cpptraj able to identify coordinates written by VMD?

From: Karl Debiec <ktd3.pitt.edu>
Date: Thu, 2 Jul 2015 13:31:48 -0400

Hi all,

I'm having difficulty reading Amber text coordinate files that have been
written by VMD.

I'm using cpptraj to analyze a set of trajectories run on Anton. My
previous pipeline for getting them into cpptraj was to use VMD to convert
them from Anton's binary format to Amber's text coordinate format (what VMD
calls 'crd'), and then use cpptraj to convert them to netcdf (which VMD
cannot write to directly). VMD's output is as follows:

TITLE : Created by VMD with 1231 atoms
  -6.272 6.912 -11.783 -5.600 7.013 -10.996 -6.985 7.648 -11.604
   7.198 -12.581 -6.762 5.529 -11.918 -7.619 5.628 -12.567 -5.743
  21.927 4.188 -8.388 20.894 5.228 -10.236 20.653 4.187 -10.673
   6.244 -10.947 20.922
  62.856 62.856 62.856
  -5.770 6.134 -11.699 -5.159 6.220 -10.862 -6.524 6.822 -11.501

However, cpptraj does not recognize these files as Amber coordinates,
instead trying to read them as Tinker coordinates and failing:

  [trajin 0000_solute.crd ]
        Reading '0000_solute.crd' as Tinker file
Error: Number of atoms in Tinker file changes from 7399136 to 1231
Warning: An error occurred while determining number of frames in Tinker
Warning: Will attempt to read -1 frames.
       Tinker file 0000_solute.crd has -1 frames.
Error: Could not set up 0000_solute.crd for reading.
Error: Could not set up input trajectory '0000_solute.crd'

Using earlier versions of cpptraj (and VMD), though I don't know exactly
which versions, I was able to convert the coordinates in this manner, but
in the latest development version (from the gitosis git repo), I obtain the
above error.

I've adjusted my pipeline to instead have VMD convert them to Gromacs trr,
which cpptraj recognizes properly. This is probably better, as it should
retain more precision than the text intermediate (I think), but I thought
it was worth asking the list if this behavior (cpptraj may not recognize
Amber coordinates written by VMD) is known.

Thank you,
Karl Debiec

Karl Debiec
Graduate Student, Molecular Biophysics & Structural Biology
University of Pittsburgh
Chong Group, Department of Chemistry
Gronenborn Group, Department of Structural Biology
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Received on Thu Jul 02 2015 - 11:00:02 PDT
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