[AMBER] error in mmpbsa

From: Fransiska Kurniawan <siska.fa.itb.ac.id>
Date: Fri, 19 Jul 2019 16:24:16 +0700 (WIB)

Dear all,

I run the MMPBSA calculation and it never finished. I got error and when I check the output file, and here is the suspected error..

Processing frame 1
      iter Total bad vdW elect nonpolar genBorn frms
               eff.c(2717) enb14 --> -nan
               eff.c(2718) eel14 --> -nan
               eff.c(2776) enb --> -nan
               eff.c(2777) eel --> -nan
               eff.c(2778) e_gb --> -9175.414
               eff.c(2779) esurf --> 0.000
               eff.c(2780) evdwnp --> 0.000
ff: 0 -nan -nan -nan -nan 0.00 -9175.41 -nan
 BOND = 12918940.9380 ANGLE = -nan DIHED = -nan
 VDWAALS = -nan EEL = -nan EGB = -9175.4138
 1-4 VDW = -nan 1-4 EEL = -nan RESTRAINT = 0.0000
 ESURF = 0.0000

The error in the command :
Beginning PB calculations with /home/aurora/amber16/bin/mmpbsa_py_energy
  calculating complex contribution...
  File "/home/aurora/amber16/bin/MMPBSA.py.MPI", line 100, in <module>
  File "/home/aurora/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/home/aurora/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/home/aurora/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 433, in run
    self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError: /home/aurora/amber16/bin/mmpbsa_py_energy failed with prmtop complex.prmtop!
        PB bomb in pb_setgrd(): Allocation aborted

Error occured on rank 1.
Exiting. All files have been retained.

Anyone can help me to overcome this problem?

I already check the prmtop file but there is no problem with it.. I already check it using VMD and the number of atoms also correct.

Thank you.


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Received on Fri Jul 19 2019 - 02:30:04 PDT
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