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
