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
startframe=150, endframe=9999, interval=6,
strip_mask= :WAT:CLA:SOD,
# entropy=1,
/
&gb
igb=2, saltcon=0.154,
# MMPBSA.py -O -i mmpbsa.in -o result.dat -sp step3_input.parm7 -cp
complex.prmtop -rp receptor.prmtop -lp LIG.prmtop -y
/mnt/c/charmm-gui-1690986943/namd/*.mdcrd
This is the output that I get:
Loading and checking parameter files for compatibility...
CHAMBER prmtops found. Forcing use of sander
cpptraj found! Using /home/mehizia/amber20_src/bin/cpptraj
sander found! Using /home/mehizia/amber20_src/bin/sander
Preparing trajectories for simulation...
153 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with /home/mehizia/amber20_src/bin/sander
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning PB calculations with /home/mehizia/amber20_src/bin/sander
calculating complex contribution...
File "/home/mehizia/amber20_src/bin/MMPBSA.py", line 100, in <module>
app.run_mmpbsa()
File
"/home/mehizia/amber20_src/lib/python3.8/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/home/mehizia/amber20_src/lib/python3.8/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/home/mehizia/amber20_src/lib/python3.8/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'
Exiting. All files have been retained.
did I do anything wrong?
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Received on Sun Apr 18 2021 - 04:00:02 PDT
