[AMBER] Found an invalid periodicity in the prmtop file : MMPBSA

From: venkat <azbvenkat.gmail.com>
Date: Wed, 11 Dec 2019 21:43:02 +0530

Hello Everyone,
I am trying to run the MMPBSA calculation, for my protein + Ag13
nanoparticle complex (Ag13 LJ parameter assigned manually by me and md
performed in gromacs. Then converted parm into amber form using parmed ),
but getting error as follows "Found an invalid periodicity in the prmtop
file: " I searched mailing list related issue found (http://archive.ambermd
.org/201205/0450.html , http://archive.ambermd.org/201205/0419.html), and
understood Dihedral value is zero affecting run. For remove that, I bit
confused, checked in the note pad , flag name DIHEDRAL_PHASE (many of them
is zero) and DIHEDRAL_PERIODICITY (none of them is zero).
here I expecting your guidance to handle this issue.

Kindly get the files in attachment link

Error as follows:
python2.7 /opt/amber16/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA
.dat -sp FULL-AG13-ONE.top -cp complex.prmtop -rp receptor.prmtop -lp
ligand.prmtop -y LAST5NS-FULL-AG13-ONE.dcd
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /opt/amber16/bin/mmpbsa_py_energy
cpptraj found! Using /opt/amber16/bin/cpptraj
Preparing trajectories for simulation...
50 frames were processed by cpptraj for use in calculation.

Running calculations on normal system...

Beginning GB calculations with /opt/amber16/bin/mmpbsa_py_energy
  calculating complex contribution...
*Found an invalid periodicity in the prmtop file: 727*
  File "/opt/amber16/bin/MMPBSA.py", line 100, in <module>
  File "/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
218, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/opt/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 157, in run
CalcError: /opt/amber16/bin/mmpbsa_py_energy failed with prmtop complex.
Exiting. All files have been retained.

Thank you
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Received on Wed Dec 11 2019 - 08:30:02 PST
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