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
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
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> > >
> > > _______________________________________________
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> > > 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
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> 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 Fri May 18 2012 - 11:30:02 PDT
