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
