Dear Ambr experts,
I am trying to use MMPBSA.py.MPI program to get binding
affinities. I am using amber20tools for this purpose.
I ran 5 independent simulations of a protein ligand
complex, I want run MM/PBSA calcualtions on each these simulations.
*The input files I am using are:*
>
> * &general*
> * startframe=200, endframe=600, interval=10, verbose=2, ligand_mask=:LIG
> strip_mask=:WAT,Na+,Cl-, keep_files=1,*
> */*
> *&pb*
> * istrng=0.00, fillratio=4.0, inp=1, radiopt=0,*
> */*
>
> 1. While executing the frames it gives me the error as follows:
>
>
- File "/home/deva/softwares/amber20_src/bin/MMPBSA.py.MPI", line 100,
in <module>
app.run_mmpbsa()
File
"/home/deva/softwares/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/deva/softwares/amber20_src/lib/python3.8/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/home/deva/softwares/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.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=1
:
system msg for write_line failure : Bad file descriptor
2. Despite the error messageabove program ran fine in case of simulation 1.
But, for sencond independent simulations it didnot give output file
(FINAL_RESULTS_MMPBSA.dat). Then I looked into the files generated by
MMPBSA, it did not create "_MMPBSA_ligand_pb.mdout.0". The trajectory
files given as input for these calculations are of the size.
3. In some cases I found the following in the mdout files, the calculations
were not done.
Processing frame 1
iter Total bad vdW elect nonpolar EPB
frms
eff.c(2675) enb14 --> -nan
eff.c(2676) eel14 --> -nan
Can anyone of you help me to figure out this?
Thanks,
Divya.
The executable is giving me the following error
Dr. Divya Bharathi,
Post Doctoral Fellow,
IIIT
Hyderabad-500032.
INDIA.
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Received on Thu Dec 03 2020 - 00:00:02 PST
