Dear Amber Experts,
I’m trying to run parallel MMPBSA calculations on a ligand binding trajectory.
Here’s the input file:
Input file for running PB and GB
&general
verbose=2,
strip_mask=:Na+,Cl-,
ligand_mask=:EGC,
netcdf=1,
interval=10,
entropy=1
/
&pb
istrng=0.15,
fillratio=4.0
/
&nmode
nmode_istrng=0.15,
/
And this is the command I issue:
mpirun -np 4 MMPBSA.py.MPI -O -i mmpbsa.in \
-sp stripped.prmtop \
-cp complex.prmtop -rp receptor.prmtop \
-lp ligand.prmtop -eo energies.csv -y Production.nc
This is the output that I get:
Loading and checking parameter files for compatibility...
cpptraj found! Using /usr/local/amber16/bin/cpptraj
mmpbsa_py_energy found! Using /usr/local/amber16/bin/mmpbsa_py_energy
mmpbsa_py_nabnmode found! Using /usr/local/amber16/bin/mmpbsa_py_nabnmode
Preparing trajectories for simulation...
About to call autoimage
Autoimage should have been called
125 frames were processed by cpptraj for use in calculation.
125 frames were processed by cpptraj for nmode calculations.
Running calculations on normal system...
Beginning PB calculations with /usr/local/amber16/bin/mmpbsa_py_energy
calculating complex contribution...
/usr/local/amber16/lib/python3.6/site-packages/MMPBSA_mods/main.py:604: UserWarning: ligand_mask overwritten with default
warnings.warn('ligand_mask overwritten with default\n')
File "/usr/local/amber16/bin/MMPBSA.py.MPI", line 100, in <module>
app.run_mmpbsa()
File "/usr/local/amber16/lib/python3.6/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/usr/local/amber16/lib/python3.6/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/usr/local/amber16/lib/python3.6/site-packages/MMPBSA_mods/calculation.py", line 428, in run
error_list = [s.strip() for s in out.split('\n')
TypeError: a bytes-like object is required, not 'str'
Error occured on rank 0.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
Am I doing anything wrong? What’s weird is that an MMGBSA calculation with the following inputs runs fine:
Input file for running PB and GB
&general
verbose=2,
strip_mask=:Na+,Cl-,
ligand_mask=:EGC,
netcdf=1,
interval=10
/
&gb
igb=5,
saltcon=0.150
/
My machine is a macOS High Sierra v. 10.13.4.
Note: I have not updated to ambertools 18 since I’m using a manually modified and re-compiled from source version of the MMPBSA.py program that avoids calling the autoimage command: see this thread of mine from awhile ago (http://archive.ambermd.org/201702/0101.html) for an explanation.
Thanks for any help!
Juan
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Received on Mon Apr 30 2018 - 11:00:03 PDT
