[AMBER] Found an invalid periodicity in the prmtop file: ... CalcError: bin/mmpbsa_py_energy failed with prmtop .prmtop!

From: Harold Grosjean <haroldgrosjean.gmail.com>
Date: Tue, 10 Mar 2020 17:47:02 +0000

Hello Everybody,

I am trying to perform MMGBSA calculation on a simulation of a
protein-ligand system. When I try to run the MMPBSA.py command on my
terminal - the error bellow is returned.

My "master" topology file was translated with gromber and then "stripped"
with: ante-MMPBSA.py -p complex.prmtop -c prot-lig-ant2.prmtop -r
prot-ant2.prmtop -l lig-ant2.prmtop -s :CL:NA:SOL -n :LIG

The VERY strange thing is that the calculation runs without problems when
the "use_sander=1" is present in my mmpbsa.in file. The following error
appears when I remove it,


*MMPBSA.py -O -i mmpbsa.in <http://mmpbsa.in> -o FINAL_RESULTS_MMPBSA.dat
-sp complex.prmtop -cp prot-lig-ant2.prmtop -rp prot-ant2.prmtop -lp
lig-ant2.prmtop -y trajectory.ncdf*

*Loading and checking parameter files for compatibility...*

*mmpbsa_py_energy found! Using bin/mmpbsa_py_energy*

*cpptraj found! Using 2020/amber18/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

* calculating complex contribution...*

*Found an invalid periodicity in the prmtop file: 285*

* File "Linux_x86_64/amber/19/Jan2020/amber18/bin/MMPBSA.py", line 100, in

* app.run_mmpbsa()*

* File
line 218, in run_mmpbsa*

* self.calc_list.run(rank, self.stdout)*

* File
line 82, in run*

* calc.run(rank, stdout=stdout, stderr=stderr)*

* File
line 157, in run*

* self.prmtop))*

*CalcError: bin/mmpbsa_py_energy failed with prmtop prot-lig-ant2.prmtop!*
*Exiting. All files have been retained*

Any help would be much appreciated as I have been trying to debug this for
a substantial amount of time now.


*Harold Grosjean*

D.Phil Candidate in Structural Biology

University of Oxford - Department of Biochemistry
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Received on Tue Mar 10 2020 - 11:00:02 PDT
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