[AMBER] mmpbsa error

From: Mehreen Ghufran <mehreen.awkum.edu.pk>
Date: Wed, 6 Feb 2019 21:19:55 +0500

Dear Amber users
kindly anyone help me please. i have got this type of error (mentioned
below) in calculating mmpbsa energy since dec 2018 but after searching alot
still didnot find any solution..please could anyone help me.why i got
prmtop error in complex-nowater.prmtop file..

mmpbsa error

linux-njex:/home/awd/2-revised # MMPBSA.py -O -immpbsa.in -o
FINAL-RESULTS-MMPBSA.dat -sp complex-water.prmtop -cp
complex-nowater.prmtop -rp rec.prmtop -lp pep.prmtop -y md50.mdcrd
Loading and checking parameter files for compatibility...

mmpbsa_py_energy found! Using /opt/amber18/bin/mmpbsa_py_

cpptraj found! Using /opt/amber18/bin/cpptraj

Preparing trajectories for simulation...

50 frames were processed by cpptraj for use in

Running calculations on normal system...

Beginning GB calculations with /opt/amber18/bin/mmpbsa_py_

  calculating complex contribution...

  File "/opt/amber18/bin/MMPBSA.py", line 100, in


  File "/opt/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line
218, in run_mmpbsa

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

  File "/opt/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run

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

  File "/opt/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 157, in run


CalcError: /opt/amber18/bin/mmpbsa_py_energy failed with prmtop

On Wednesday, February 6, 2019, David A Case <david.case.rutgers.edu> wrote:

> On Wed, Feb 06, 2019, Anthony Cruz-Balberdy wrote:
> >
> >I'm trying to simulate the aggregation of 300 small molecules into a
> >nanostructure. I started the simulation with simulation box big enough so
> >that the molecules were not too close together. During the simulation, the
> >molecules started to aggregate and started forming the nanostructure that
> I
> >was expecting. The only problem is that the nanostructure is open in the
> >middle because the top part of the structure is touching the top of the
> box
> >and the bottom part of the structure is touching the bottom of the box
> >(along the z-axis). I think that if the box size change along the z-axis,
> >the nanostructure will be able to close itself.
> Are you sure this is not an imaging problem? Try playing with the image
> command in cpptraj to see if you can just change the location of the
> unit cell boundaries to get what you want.
> ....dac
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Received on Wed Feb 06 2019 - 08:30:02 PST
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