quantaosun / ambertools-openmm-md Goto Github PK

If enconter potential openmm error, libstdc++.so.6: version GLIBCXX_3.4.30' not found` #2886

Please refer to

microsoft/DeepSpeed#2886

Hi @quantaosun,

I use your notebook to running MMGBSA calculation. I reach the last step when using MMGBSA.py to run.

I create mmpbsa.in by using:

f = open("mmpbsa.in", "w")
f.write("""&general """  + "\n"
"""  endframe=""" + """,  interval=""" + """, strip_mask=:WAT:Na+:Cl-:Mg+:K+, """ + "\n"
"""/ """ + "\n"
"""&gb """ + "\n"
""" igb=""" +  """, saltcon=""" +  """, """ + "\n"
"""/""")
f.close()

The error is:

  File "/usr/local/bin/MMPBSA.py", line 90, in <module>
    app.read_input_file()
  File "/usr/local/lib/python3.10/site-packages/MMPBSA_mods/main.py", line 762, in read_input_file
    self.INPUT = self.input_file.Parse(infile)
  File "/usr/local/lib/python3.10/site-packages/MMPBSA_mods/input_parser.py", line 443, in Parse
    SetValue(var[1])
  File "/usr/local/lib/python3.10/site-packages/MMPBSA_mods/input_parser.py", line 112, in SetValue
    self.value = self.datatype(value)
ValueError: invalid literal for int() with base 10: ''

Fatal Error! 
All files have been retained for your error investigation: 
You should begin by examining the output files of the first failed calculation.
Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
manual for file naming conventions.

My files here:
MMGBSA_input.zip

Please help me to fix this error. Thank you very much,

from simtk.openmm import *
from simtk.openmm.app import *
from simtk.unit import *
from sys import stdout
from openmm.app import PDBFile # for final frame pdb generation

or

from openmm import *
from openmm.app import *
from openmm.unit import *
from sys import stdout
from openmm.app import PDBFile # for final frame pdb generation

Due to different openmm versions, you might need to modify the openmm python script if you try to launch a simulation within bash terminals.

In the final step, I faced with the following error, can you help me figure out my problem?

Error: Error(s) occurred during execution.
File "/usr/local/bin/MMPBSA.py", line 99, in
app.file_setup()
File "/usr/local/lib/python3.10/site-packages/MMPBSA_mods/main.py", line 161, in file_setup
self.numframes, self.numframes_nmode = make_trajectories(INPUT, FILES,
File "/usr/local/lib/python3.10/site-packages/MMPBSA_mods/make_trajs.py", line 59, in make_trajectories
traj = Trajectory(FILES.solvated_prmtop, FILES.mdcrd, cpptraj)
File "/usr/local/lib/python3.10/site-packages/MMPBSA_mods/make_trajs.py", line 506, in init
self.Query()
File "/usr/local/lib/python3.10/site-packages/MMPBSA_mods/make_trajs.py", line 641, in Query
raise TrajError('%s failed when querying %s' % (self.exe, traj))
TrajError: /usr/local/bin/cpptraj failed when querying prot_lig_prod_all.dcd

I found your code is used for running MMPBSA with openMM.

Please help me to run MMGBSA. Thank you very much.

https://github.com/quantaosun/Ambertools-OpenMM-MD/blob/main/Ambertools-OpenMM-MD_GBSA.ipynb