Dear all,I am trying to do the mmpbsa analysis on a 1ns trajectory. when i run MMPBSA.py i get the following error..............................................Loading and checking parameter files for compatibility... mmpbsa_py_energy found! Using /mnt/d/amber18/bin/mmpbsa_py_energy cpptraj found! Using /mnt/d/amber18/bin/cpptraj Preparing trajectories for simulation... [LAPTOP-C5K9759P:00320] 5 more processes have sent help message help-btl-vader.txt / cma-permission-denied [LAPTOP-C5K9759P:00320] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages 100 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with /mnt/d/amber18/bin/mmpbsa_py_energy calculating complex contribution... mmpbsa_py_energy: malloc.c:2401: sysmalloc: Assertion `(old_top == initial_top (av) && old_size == 0) || ((unsigned long) (old_size) >= MINSIZE && prev_inuse (old_top) && ((unsigned long) old_end & (pagesize - 1)) == 0)' failed. File "/mnt/d/amber18//bin/MMPBSA.py.MPI", line 100, in app.run_mmpbsa() File "/mnt/d/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa self.calc_list.run(rank, self.stdout) File "/mnt/d/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run calc.run(rank, stdout=stdout, stderr=stderr) File "/mnt/d/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 157, in run self.prmtop)) CalcError: /mnt/d/amber18/bin/mmpbsa_py_energy failed with prmtop receptor.gas.prmtop! Error occured on rank 5. Exiting. All files have been retained. .................................................................................................
I created the prmtop file atleast twice but same error. Is it a memory error?I also read through the list and made all the topology files again with PBRadii mbondi2 as the igb=2 in the file i used from the tutorial. Then I tried using the MMPBSA.pl then the following error results
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At line 434 of file make_crd_hg.F (unit = 5, file = 'stdin') Fortran runtime error: Bad value during floating point read.
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I looked the error. the answer was to look for any strange characters in the trajectory file. when I do the grep command it says binary matches and the nothing else. What am i doing wrong.? I am attaching my files. "mmpbsa_1" is for MMPBS.py and "mmpbsa.in" is to run the perl script.
Thank you
Regards
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