Dear AMBERs,
I run a standard protocol for MM-GBSA free energy decomposition (see the
file at the end of my e-mail) and encounter this problem: although GB
works without any errors and produces normal output, I get an empty
decomposition output, which looks like this:
-------------------
| Run on Tue Sep 26 08:05:19 2017
| GB non-polar solvation energies calculated with gbsa=
-------------------
I am sure that there are no problems with the topologies because there
are no strange values in the GB output.
Temporary files _MMPBSA* are not deleted, and the reported error is the
following:
-------------------
File "/users/work/czarek/amber16/bin/MMPBSA.py.MPI", line 109, in
<module>
app.write_final_outputs()
File
"/users/work/czarek/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 645, in write_final_outputs
self.normal_system, self.mutant_system, self.mut_str, self.pre)
File
"/users/work/czarek/amber16/lib/python2.7/site-packages/MMPBSA_mods/output_file.py",
line 673, in write_decomp_binding_output
gb_bind.parse_all()
File
"/users/work/czarek/amber16/lib/python2.7/site-packages/MMPBSA_mods/amber_outputs.py",
line 2112, in _parse_all_csv
self._parse_all_begin()
File
"/users/work/czarek/amber16/lib/python2.7/site-packages/MMPBSA_mods/amber_outputs.py",
line 2015, in _parse_all_begin
com_token = self.com.get_next_term(searched_token, framenum)
File
"/users/work/czarek/amber16/lib/python2.7/site-packages/MMPBSA_mods/amber_outputs.py",
line 1536, in _get_next_term
internal = float(line[11:20])
ValueError: could not convert string to float: *********
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
-------------------
If I do decomposition on frames one by one separately, it works for some
frames without problems but not for others (for the problematic single
frames I get the same empty output as shown above). Trajectory
(visually) looks fine, there is no sign of corrupted frames, RMSD and
other parameters obtained by cpptraj do not seem to be problematic. I
tried also to rewrite the trajectory into the the old format but the out
come was identical.
My input:
-------------------------------
Input file for GB/decomposition calculation
&general
startframe=1, endframe=1000, interval=1,
verbose=2, keep_files=0,
/
&gb
igb=2,
/
&decomp
idecomp=2
/
-------------------------------
I run MMPBSA in a standard way with all four topogies:
MMPBSA.py.MPI -O -i decomp.input -o gb_binding.out -cp complex.top -rp
receptor.top -lp ligand.top -sp ../top.top -y ../mdcrd/md.mdcrd
Thank you very much and cheers,
Sergey
--
Sergey Samsonov, PhD
Project Leader at Laboratory of Molecular Modeling,
Department of Theoretical Chemistry,
Faculty of Chemistry,
University of Gdansk
ul. Wita Stwosza 63
80-308 Gdansk, Poland
phone: +48 58 523 5166
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Received on Tue Sep 26 2017 - 00:30:03 PDT
