Dear Amber Users,
I am using MMGBSA.py script to calculate the binding free energy
between a DNA-protein system. I am getting the following error. Ligand
(DNA) contains 2 residues and receptor (protein) contains 435
resiues.. I have included 500 snapshots for analysis...
I cannot understand the error,. I beleive my topology files are
correct
Activated Environment for using: Intel MKL v10.2.6.038.
Activated environment for using: Intel Compilers, version 11.1 (073)
Activated environment for using: OpenMPI, version 1.4.3
Activated Environment for using: Intel MKL v10.2.6.038.
Activated environment for using: Intel Compilers, version 11.1 (073)
Activated environment for using: OpenMPI, version 1.4.3
checkCoordinates(): Could not predict number of frames for AMBER
trajectory file: _MMPBSA_complex.mdcrd
If this is not a compressed file then there is a problem
checkCoordinates(): Could not predict number of frames for AMBER
trajectory file: _MMPBSA_complex.mdcrd
If this is not a compressed file then there is a problem
checkCoordinates(): Could not predict number of frames for AMBER
trajectory file: _MMPBSA_complex.mdcrd
If this is not a compressed file then there is a problem
checkCoordinates(): Could not predict number of frames for AMBER
trajectory file: _MMPBSA_complex.mdcrd
If this is not a compressed file then there is a problem
checkCoordinates(): Could not predict number of frames for AMBER
trajectory file: _MMPBSA_complex.mdcrd
If this is not a compressed file then there is a problem
checkCoordinates(): Could not predict number of frames for AMBER
trajectory file: _MMPBSA_complex.mdcrd
If this is not a compressed file then there is a problem
sh: line 1: 11050 Segmentation fault
/g/software/lms/amber11/exe/ptraj com.prmtop
_MMPBSA_ptrajentropy.in > _MMPBSA_ptraj_entropy.out
Error! Ptraj failed. Check coordinate and topology files for the
complex.
Error! Ptraj failed. Check coordinate and topology files for the
complex.
Error! Ptraj failed. Check coordinate and topology files for the
complex.
Error! Ptraj failed. Check coordinate and topology files for the
complex.
Error! Ptraj failed. Check coordinate and topology files for the
complex.
Error! Ptraj failed. Check coordinate and topology files for the
complex.
Error! Ptraj failed. Check coordinate and topology files for the
complex.
checkCoordinates(): Could not predict number of frames for AMBER
trajectory file: _MMPBSA_complex.mdcrd
If this is not a compressed file then there is a problem
checkCoordinates(): Could not predict number of frames for AMBER
trajectory file: _MMPBSA_complex.mdcrd
If this is not a compressed file then there is a problem
checkCoordinates(): Could not predict number of frames for AMBER
trajectory file: _MMPBSA_complex.mdcrd
If this is not a compressed file then there is a problem
checkCoordinates(): Could not predict number of frames for AMBER
trajectory file: _MMPBSA_complex.mdcrd
If this is not a compressed file then there is a problem
checkCoordinates(): Could not predict number of frames for AMBER
trajectory file: _MMPBSA_receptor.mdcrd
If this is not a compressed file then there is a problem
=>> PBS: job killed: mem job total 27153656 kb exceeded limit 8388608
kb
mpirun: killing job...
--------------------------------------------------------------------------
mpirun was unable to cleanly terminate the daemons on the nodes shown
below. Additional manual cleanup may be required - please refer to
the "orte-clean" tool for assistance.
--------------------------------------------------------------------------
node307
node308
~
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Received on Tue Jul 19 2011 - 14:00:03 PDT
