[AMBER] mmpbsa problem with OPC waters

From: Antonija Tomić via AMBER <amber.ambermd.org>
Date: Mon, 24 Oct 2022 13:15:42 +0200

Dear Amber Users,

I have the similar problem as already asked on the mailing list
(http://archive.ambermd.org/202109/0046.html).
Namely I try to run mmpbsa analysis with a couple of explicit water
molecules defined as part of the complex. This worked fine when working
with trajectories (and .prmtop) that had been generated using ff14SB +
TIP3P but seems to no longer work when using trajectories generated with
ff19SB + OPC.


I use the following script (:WAT are removed from strip_mask as analysis
is preformed on already striped trajectory - trajectory with defined
number of water molecules and prepared by closest command):

Input file
&general
  interval=5,
  verbose=2, keep_files=0,
  startframe=1801,
  endframe=2000,
  strip_mask=:Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL,
  /
  &gb
  igb=5, saltcon=0.020,
  /
&pb
   indi=2, istrng=0.020, radiopt=0,
  /

Job performed with ff19sb + opc stops with the following error:

Running calculations on normal system...

Beginning GB calculations with /usr/local/amber20/bin/mmpbsa_py_energy
   calculating complex contribution...
   calculating receptor contribution...
   calculating ligand contribution...

Beginning PB calculations with /usr/local/amber20/bin/mmpbsa_py_energy
   calculating complex contribution...
   File "/usr/local/amber20/bin/MMPBSA.py.MPI", line 100, in <module>
     app.run_mmpbsa()
   File
"/usr/local/amber20/lib/python3.9/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
     self.calc_list.run(rank, self.stdout)
   File
"/usr/local/amber20/lib/python3.9/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
     calc.run(rank, stdout=stdout, stderr=stderr)
   File
"/usr/local/amber20/lib/python3.9/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.

I must emphasize that I have no problem visualizing the trajectories of
the complex, receptor and ligand in VMD.
I have radiopt=0 in my PB namelist as suggested
http://archive.ambermd.org/202006/0130.html).

Generated gb.mdout and pb.mdout files have:
enb --> -nan
eel --> -nan

Does anyone know how to handle this problem?

Kind regards,

PhD Antonija Tomić
LBPMM, Institut Ruđer Bošković
Bijenička cesta 54, 10000 Zagreb, Croatia

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Received on Mon Oct 24 2022 - 04:30:02 PDT
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