Hi Bill, Actually, I compiled Amber/AmberTools after cloning the AMBER git repo, so I'm no quite sure.At the start of MMPBSA.py, however, it says that the file was last updated 10/31/2011.So I should probably recompile after doing a new git pull. Do you think that will solve the problem? Best regards,
Åge > From: brmilleriii.gmail.com
> Date: Fri, 18 May 2012 09:11:30 -0400
> To: amber.ambermd.org
> Subject: Re: [AMBER] Output from pairwise decomposition with MMPBSA.py(.MPI)
>
> What version of Amber/AmberTools are you using?
>
> -Bill
>
>
>
> On May 18, 2012, at 9:01 AM, Åge Skjevik <aage.dark.hotmail.com> wrote:
>
> >
> >
> >
> >
> > 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 18 2012 - 07:30:04 PDT
