Hello all
I am facing problem in calculation of per residue decomposition energy. I
am running following command on mdcrd files. The MMGBSA and MMPBSA have
been successfully completed but the decompostion.dat file is empty and
following command exits with an error as mentioned below:
*MMPBSA.py -i mmgbsa.in <
http://mmgbsa.in> -o explicit.dat -sp
complex-box.prmtop -cp complex.prmtop -rp receptor.prmtop -lp ligand.prmtop
-y ../sim1_clq_complex.mdcrd*
Loading and checking parameter files for compatibility...
cpptraj found! Using /home/ravi/anaconda3/bin/cpptraj
sander found! Using /home/ravi/anaconda3/bin/sander
Preparing trajectories for simulation...
10 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with /home/ravi/anaconda3/bin/sander
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning PB calculations with /home/ravi/anaconda3/bin/sander
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
File "/home/ravi/anaconda3/bin/MMPBSA.py", line 109, in <module>
app.write_final_outputs()
File
"/home/ravi/anaconda3/lib/python3.5/site-packages/MMPBSA_mods/main.py",
line 645, in write_final_outputs
self.normal_system, self.mutant_system, self.mut_str, self.pre)
File
"/home/ravi/anaconda3/lib/python3.5/site-packages/MMPBSA_mods/output_file.py",
line 673, in write_decomp_binding_output
gb_bind.parse_all()
File
"/home/ravi/anaconda3/lib/python3.5/site-packages/MMPBSA_mods/amber_outputs.py",
line 2112, in _parse_all_csv
self._parse_all_begin()
File
"/home/ravi/anaconda3/lib/python3.5/site-packages/MMPBSA_mods/amber_outputs.py",
line 2015, in _parse_all_begin
com_token = self.com.get_next_term(searched_token, framenum)
File
"/home/ravi/anaconda3/lib/python3.5/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.
######mmgbsa.in##### <
http://mmgbsa.in#%23%23%23%23>
Per-residue GB and PB decomposition
&general
startframe=1, endframe=20000, verbose=2000,
/
&gb
igb=5, saltcon=0.100,
/
&pb
istrng=0.100,
/
&decomp
idecomp=1, print_res="1-306"
dec_verbose=1,
/
###########################
Have checked mailing list which suggest the problem occurs with old Amber
version before 11 but I am already calculating with Ambertools19.
So, can anyone help me out in finding the problem?
Thanks and regards
Shivangi Agarwal
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Received on Sat Sep 07 2019 - 13:00:02 PDT
