Hello
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_
energy
cpptraj found! Using /opt/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 /opt/amber18/bin/mmpbsa_py_
energy
calculating complex contribution...
File "/opt/amber18/bin/MMPBSA.py", line 100, in
<module>
app.run_mmpbsa()
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
self.prmtop))
CalcError: /opt/amber18/bin/mmpbsa_py_energy failed with prmtop
complex-nowater.prmtop!
<
https://mail.google.com/mail/u/0/s/?view=att&th=168b7d2a5ce1436b&attid=0.1&disp=attd&realattid=f_jrq4nqnt0&safe=1&zw>
complex-nowater.prmtop
<
https://mail.google.com/mail/u/0/s/?view=att&th=168b7d2a5ce1436b&attid=0.1&disp=attd&realattid=f_jrq4nqnt0&safe=1&zw>
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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>
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Received on Wed Feb 06 2019 - 08:30:02 PST
