[AMBER-Developers] ptraj errors

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 2 Oct 2009 17:16:12 -0400

Hello everybody,

Recent versions of ptraj that I have checked out of the tree, the latest one
being this morning, have failed to create mdcrds, often throwing a "Floating
point exception". When I go to the ptraj_comprehensive test directory and
run Run.comprehensive, I get the following output:

ptraj: Test multiple ptraj actions.
diffing dist_end_to_end.list.save with dist_end_to_end.list
PASSED
==============================================================
diffing omega.save with omega
PASSED
==============================================================
diffing phi.save with phi
PASSED
==============================================================
diffing psi.save with psi
PASSED
==============================================================
diffing watershell.list.save with watershell.list
PASSED
==============================================================
diffing test.mdcrd.save with test.mdcrd
possible FAILURE: check test.mdcrd.dif
==============================================================
ptraj was not built with NetCDF support - skipping this test.

The 'possible failure' at the bottom was quite severe. I'll paste the
entire test.mdcrd file that was created:

swails.Batman:~/newamber/10.02.09/amber11/test/ptraj_comprehensive$ cat
test.mdcrd
trajectory generated by ptraj
swails.Batman:~/newamber/10.02.09/amber11/test/ptraj_comprehensive$

Which is evidence that no trajectory file was in fact created. The end of
ptraj.out showed

PTRAJ: strip :WAT
Mask [:WAT] represents 4731 atoms

PTRAJ: trajout test.mdcrd

PTRAJ: Successfully read the input file.
       Coordinate processing will occur on 100 frames.
       Summary of I/O and actions follows:

INPUT COORDINATE FILES
  File (trajectory.mdcrd) is an AMBER trajectory (with box info) with 100
sets

OUTPUT COORDINATE FILE
  File (test.mdcrd) is an AMBER trajectory (with box info)
ACTIONS
  1> 2> 3> 4> DISTANCE: between the atoms selections center of mass will
be
      saved to array named end_to_end
  5> RMS to first frame using no mass weighting
      Atom selection follows * (All atoms are selected)
  6> CENTER to origin via center of geometry, atom selection follows :1-7
  7> IMAGE by molecule to origin using the center of mass, atom
selection * (All atoms are selected)
  8> WATER SHELL: Output to watershell.list
      The first shell will contain water < 3.400 angstroms from
      the solute; the second shell < 5.000 angstroms...
      The solute atoms are :1-7
      The solvent atoms are :8-1584
  9> STRIP: 4731 atoms will be removed from trajectory: :8-1584


Processing AMBER trajectory file trajectory.mdcrd

 1% ............ 25% ............ 50% ............ 75% ............ 100%


PTRAJ: Successfully read in 100 sets and processed 100 sets.

Dumping accumulated results (if any)

PTRAJ WATERSHELL: dumping data to output file

It seems like it's stopping short of executing the trajout command.

Any thoughts?

Thanks!
Jason Swails
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Received on Fri Oct 02 2009 - 14:30:01 PDT
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