Can you send a copy of your input files including a test trajectory with a
couple of frames? I will try it and see if I can reproduce your error on my
local machine.
-Bill
On Mon, May 21, 2012 at 5:56 PM, Åge Skjevik <aage.dark.hotmail.com> wrote:
>
> Hi again Bill, I did a git pull and recompiled MMPBSA.py from the
> src/mmpbsa_py/ folder. However, the problem persists: Reading command-line
> arguments and input files...
> Loading and checking parameter files for compatibility...
> File "/usr/local/amber/bin/MMPBSA.py", line 641, 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.
> Exiting. All files have been retained.
> The calculation itself finished successfully. Best regards, Åge
> > Date: Fri, 18 May 2012 14:02:56 -0400
> > From: brmilleriii.gmail.com
> > To: amber.ambermd.org
> > Subject: Re: [AMBER] Output from pairwise decomposition with
> MMPBSA.py(.MPI)
> >
> > If the calculation itself worked correctly (check the all of the mdout
> > files to see if they completed all frames successfully), then you should
> be
> > able to re-compile and just use the -rewrite-outputs option. You should
> > essentially use the exact same command line (with all of the prmtop
> files,
> > input files, trajectory, etc.) specified, and then just at the end of the
> > line add "-rewrite-output".
> >
> > Re-compile the newest release and let us know if you still get the same
> > error or not.
> >
> > -Bill
> >
> > On Fri, May 18, 2012 at 1:53 PM, Åge Skjevik <aage.dark.hotmail.com>
> wrote:
> >
> > >
> > > 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
> > > > > > > _______________________________________________
> > > > > > > AMBER mailing list
> > > > > > > AMBER.ambermd.org
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> > > > > >
> > > > > > _______________________________________________
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> > > > >
> > > > > _______________________________________________
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> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Bill Miller III
> > > > Quantum Theory Project,
> > > > University of Florida
> > > > Ph.D. Graduate Student
> > > > 352-392-6715
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> > > > AMBER mailing list
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> > >
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> > >
> >
> >
> >
> > --
> > Bill Miller III
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-6715
> > _______________________________________________
> > 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
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Mon May 21 2012 - 16:00:02 PDT
