Dear AMBER users, I have run pairwise decomposition analysis with MMPBSA.py.MPI and with the following input file:
&general
startframe=1000, endframe=1999, interval=1, receptor_mask=":16-254", ligand_mask=":1-15",
verbose=1, strip_mask=":16-266,:WAT", debug_printlevel=2, keep_files=2,
/
&pb
istrng=0.15, cavity_offset=0.92,
/
&decomp
idecomp=4, print_res="1 - 254", dec_verbose=1,
/
It seems the calculations themselves complete successfully, but there isn't any output in FINAL_DECOMP_MMPBSA.dat(FINAL_RESULTS_MMPBSA.dat is normal), so there seems to be a problem with writing the output file. I get the followingerror message: Beginning PB calculations with /usr/local/amber/bin/sander
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution... File "/usr/local/amber/bin/MMPBSA.py.MPI", line 641, in <module>
mutant_system, mut_str)
File "/usr/local/amber/bin/MMPBSA_mods/output_file.py", line 807, in write_decomp_binding_output
pb_bind.parse_all()
File "/usr/local/amber/bin/MMPBSA_mods/amber_outputs.py", line 2328, in _parse_all_csv
self._parse_all_begin()
File "/usr/local/amber/bin/MMPBSA_mods/amber_outputs.py", line 2196, in _parse_all_begin
com_token = self.com.get_next_term(searched_token, framenum)
File "/usr/local/amber/bin/MMPBSA_mods/amber_outputs.py", line 1669, in _get_next_term
resnum2 = int(line[13:20])
ValueError: invalid literal for int() with base 10: '7.517'
Error occured on rank 0.
I'm aware that I may have specified too many residues in print_res, so I tried to reduce the number of residues anduse the -rewrite-output option, but then I got a different error message: File "/usr/local/amber/bin/MMPBSA.py", line 633, in <module>
[numframes, numframes_nmode], mut_str)
File "/usr/local/amber/bin/MMPBSA_mods/output_file.py", line 384, in write_binding_output
if INPUT[solv]:
KeyError: 'rismrun_std'
Error occured on rank 0.
Can anyone help me? Best regards, Åge SkjevikDepartment of BiomedicineUniversity of Bergen, Norway
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Received on Fri May 18 2012 - 06:30:04 PDT
