[AMBER] app.run_mmpbsa() and mdout files were not created

From: divyabharathi korlepara <divyabharathik938.gmail.com>
Date: Thu, 3 Dec 2020 13:09:11 +0530

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>
   line 218, in run_mmpbsa
       self.calc_list.run(rank, self.stdout)
   line 82, in run
       calc.run(rank, stdout=stdout, stderr=stderr)
   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
               eff.c(2675) enb14 --> -nan
               eff.c(2676) eel14 --> -nan

Can anyone of you help me to figure out this?


                The executable is giving me the following error
Dr. Divya Bharathi,
Post Doctoral Fellow,
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Received on Thu Dec 03 2020 - 00:00:02 PST
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