Hi again Bill, Thanks for the help. Actually, my system consists of two ligands, each bound to a monomer in a protein dimer.So I do two MMPBSA calculations, one for each ligand/monomer pair. I think it has workedaccording to plan. The _MMPBSA_complex/receptor/ligand.mdcrds look reasonable. In thiscase I strip out one ligand/monomer pair (16-266 in solvated prmtop), so that the new residue numbers for the other ligand/monomer pair are 1-254 in the complex prmtop. Per residuedecomposition has worked and seems to give reasonable results. I'm just having problems withwriting the pairwise decomposition output. Ok, so it works with that many residues. Maybe I should just try to recompile and see whathappens. If so, do you think I have to run the calculation all over again? Or can I just use the-rewrite-output option? In the latter case, what do I have to include in the MMPBSA.py command line? Best regards, Åge
> Date: Fri, 18 May 2012 11:36:07 -0400
> From: brmilleriii.gmail.com
> To: amber.ambermd.org
> Subject: Re: [AMBER] Output from pairwise decomposition with MMPBSA.py(.MPI)
>
> I am curious about your input file. You specify the ligand as residues
> 1-15, and the receptor to be residues 16-254. But then you also specify to
> strip out residues 16-266? You are running the complex and then stripping
> out the receptor coordinates before the calculation? If I am interpreting
> your input file correctly, then the program is likely to get very confused
> when it tries to calculate the energetics for the receptor and finds out
> there are no atoms there. Does this sound like what you were trying to do?
>
> Also, the number of residues you are requesting should be fine. I recently
> performed pairwise decomp on a system of 600 residues and printed out all
> residues, so the code should be able to handle it as long as your hardware
> can handle it.
>
> -Bill
>
> On Fri, May 18, 2012 at 10:07 AM, Åge Skjevik <aage.dark.hotmail.com> wrote:
>
> >
> > 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
> > > > _______________________________________________
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>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
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Received on Fri May 18 2012 - 11:00:02 PDT
