The bugfix is available on the web now.
On Wed, Feb 8, 2012 at 9:35 AM, Sangeetha B <sangeetha.bicpu.edu.in> wrote:
> Hi Jason,
>
>
> Thanks for your reply. Atlast you helped me find a solution to this
> problem. I am eagerly waiting for the bugfix release.
>
>
> --
> Thank you,
>
> With regards,
> B. Sangeetha
> Ph.D Scholar,
> Centre for Bioinformatics,
> Pondicherry University,
> Pondicherry,
> India
>
>
>
>
> On Wed, Feb 8, 2012 at 1:35 AM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> > I found the bug. I didn't catch it at first because it had already been
> > fixed in the development version. I created a bugfix for it (on
> > http://ambermd.org/bugfixesat.html) which should appear sometime in the
> > next day or two. I verified after applying that fix that it properly
> > parsed your files. It will be bugfix.27 on that page.
> >
> > Thanks for the report!
> > Jason
> >
> > On Tue, Feb 7, 2012 at 11:51 AM, Jason Swails <jason.swails.gmail.com
> > >wrote:
> >
> > > I can't see anything wrong with your nm output files. Does the
> MMPBSA.py
> > > test pass for normal mode entropy calculations?
> > >
> > > On Tue, Feb 7, 2012 at 6:52 AM, Sangeetha B <sangeetha.bicpu.edu.in
> > >wrote:
> > >
> > >> Hi,
> > >>
> > >> I am still expecting some solutions for my problem in running Normal
> > mode
> > >> analysis.
> > >>
> > >>
> > >>
> > >> --
> > >> Thank you,
> > >>
> > >> With regards,
> > >> B. Sangeetha
> > >> Ph.D Scholar,
> > >> Centre for Bioinformatics,
> > >> Pondicherry University,
> > >> Pondicherry,
> > >> India
> > >>
> > >>
> > >>
> > >> ---------- Forwarded message ----------
> > >> From: Sangeetha B <sangeetha.bicpu.edu.in>
> > >> Date: Thu, Feb 2, 2012 at 9:48 AM
> > >> Subject: Re: [AMBER] NMODE list index out of range error
> > >> To: AMBER Mailing List <amber.ambermd.org>
> > >>
> > >>
> > >> Hi,
> > >>
> > >> Thanks for the reply.. After the minimization of each frame, it says
> > >> "convergence satisfied".
> > >> I have attached all the _MMPBSA_*_nm.out files as a zipped archive
> with
> > >> this mail.
> > >>
> > >> I thank you a lot in advance. It will be very helpful if someone can
> > solve
> > >> this issue..
> > >>
> > >>
> > >> --
> > >> Thank you,
> > >>
> > >> With regards,
> > >> B. Sangeetha
> > >> Ph.D Scholar,
> > >> Centre for Bioinformatics,
> > >> Pondicherry University,
> > >> Pondicherry,
> > >> India
> > >>
> > >>
> > >> On Sat, Jan 28, 2012 at 9:12 PM, Jason Swails <jason.swails.gmail.com
> > >> >wrote:
> > >>
> > >> > Can you send your _MMPBSA_*_nm.out files so I can take a look at
> them?
> > >> >
> > >> > It appears that for some reason one of the snapshots didn't minimize
> > >> > completely and so there are different numbers of frames for the
> > complex
> > >> > receptor and ligand. However, MMPBSA should have exited more
> > gracefully
> > >> or
> > >> > readjusted silently.
> > >> >
> > >> > It may also be the case that no snapshot could minimize enough for
> the
> > >> > complex or receptor or something, so there was no data to analyze.
> > >> Again,
> > >> > the error reporting should be better.
> > >> >
> > >> > All the best,
> > >> > Jason
> > >> >
> > >> > --
> > >> > Jason Swails
> > >> > Quantum Theory Project,
> > >> > University of Florida
> > >> > Ph.D. Candidate
> > >> > 352-392-4032
> > >> >
> > >> > On Jan 28, 2012, at 1:43 AM, Sangeetha B <sangeetha.bicpu.edu.in>
> > >> wrote:
> > >> >
> > >> > > Hi,
> > >> > >
> > >> > > I have done a 5ns simulation for a protein-ligand complex and I
> want
> > >> to
> > >> > > calculate the entropy of binding for this complex using Normal
> Mode
> > >> > > analysis.
> > >> > > I have restricted my calculation to include only the residues
> within
> > >> 12
> > >> > > angstroms of the active site.
> > >> > > I run this nmode in serial in CPU mode of Tesla C2050 with a 16 GB
> > >> RAM.
> > >> > > When i run this even for something as less as 2 frames, i get the
> > >> > following
> > >> > > error.
> > >> > >
> > >> > > Reading command-line arguments and input files...
> > >> > > Loading and checking parameter files for compatibility...
> > >> > > ptraj found! Using /usr/local/amber11/bin/ptraj
> > >> > > nmode program found! Using
> /usr/local/amber11/bin/mmpbsa_py_nabnmode
> > >> > > Preparing trajectories for simulation...
> > >> > > 500 frames were read in and processed by ptraj for use in
> > calculation.
> > >> > >
> > >> > >
> > >> > > Beginning nmode calculations with mmpbsa_py_nabnmode...
> > >> > > Calculating normal modes for 2 frames
> > >> > >
> > >> > > calculating complex contribution for frame 0
> > >> > > calculating receptor contribution for frame 0
> > >> > > calculating ligand contribution for frame 0
> > >> > > calculating complex contribution for frame 1
> > >> > > calculating receptor contribution for frame 1
> > >> > > calculating ligand contribution for frame 1
> > >> > > Traceback (most recent call last):
> > >> > > File "/usr/local/amber11/AmberTools/src/mmpbsa_py/MMPBSA.py",
> line
> > >> 1344,
> > >> > > in <m
> > >> > > odule>
> > >> > > outfile.write(str(nmodenorm))
> > >> > > File
> > >> > >
> > >>
> > "/usr/local/amber11/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py"
> > >> > > , line 2263, in __str__
> > >> > > totavg, totstdev = self.AvgStdev()
> > >> > > File
> > >> > >
> > >>
> > "/usr/local/amber11/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py"
> > >> > > , line 2302, in AvgStdev
> > >> > > stdev = self._tot_stdevs()
> > >> > > File
> > >> > >
> > >>
> > "/usr/local/amber11/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py"
> > >> > > , line 2319, in _tot_stdevs
> > >> > > sum += self.com_data[0][i] - self.rec_data[0][i] -
> > >> self.lig_data[0][i]
> > >> > > IndexError: list index out of range
> > >> > >
> > >> > >
> > >> > > The input file that I used is as below:
> > >> > >
> > >> > > Input file:
> > >> > > |--------------------------------------------------------------
> > >> > > |NMODE
> > >> > > |&general
> > >> > > | verbose=1, interval=5, strip_mdcrd=0,
> > >> > > |/
> > >> > > |&nmode
> > >> > > | maxcyc=50000, nminterval=250, nmode_igb=1,
> > >> > > |/
> > >> > >
> > >> > > and the command I used to run this is
> "/usr/local/amber11/bin/MMPBSA
> > >> -i
> > >> > > nm_5e.in -cp comp_strip.prmtop -rp prot_strip.prmtop -lp
> > >> > > ligand5e_vac.prmtop -y comp5e_md1_5_12a.mdcrd"
> > >> > >
> > >> > > A file named "FINAL_RESULTS_MMPBSA.dat" is being generated but
> there
> > >> is
> > >> > no
> > >> > > Delta S value in it.. The contents of this file is shown below:
> > >> > >
> > >> > > | Run on Fri Jan 27 23:13:57 IST 2012
> > >> > >
> > >> > > |Input file:
> > >> > > |--------------------------------------------------------------
> > >> > > |NMODE
> > >> > > |&general
> > >> > > | verbose=1, interval=5, strip_mdcrd=0,
> > >> > > |/
> > >> > > |&nmode
> > >> > > | maxcyc=50000, nminterval=250, nmode_igb=1,
> > >> > > |/
> > >> > > |--------------------------------------------------------------
> > >> > > |Complex topology file: comp_strip.prmtop
> > >> > > |Receptor topology file: prot_strip.prmtop
> > >> > > |Ligand topology file: ligand5e_vac.prmtop
> > >> > > |Initial mdcrd(s): comp5e_md1_5_12a.mdcrd
> > >> > > |
> > >> > > |Best guess for receptor mask: ":1-109"
> > >> > > |Best guess for ligand mask: ":110"
> > >> > > |Ligand residue name is "UNK"
> > >> > > |
> > >> > > |Calculations performed using 500 frames.
> > >> > > |NMODE calculations performed using 2 frames.
> > >> > > |
> > >> > > |All units are reported in kcal/mole.
> > >> > > |All entropy results have units kcal/mole (Temperature is 298.15
> K).
> > >> > >
> > >> >
> > >>
> >
> -------------------------------------------------------------------------------
> > >> > >
> > >> >
> > >>
> >
> -------------------------------------------------------------------------------
> > >> > >
> > >> > >
> > >> > > Can someone please tell me what is going wrong... Is the problem
> > with
> > >> the
> > >> > > memory available in the system?
> > >> > > _______________________________________________
> > >> > > 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
> > >>
> > >>
> > >
> > >
> > > --
> > > Jason M. Swails
> > >
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Candidate
> > > 352-392-4032
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > 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
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Feb 09 2012 - 12:30:04 PST
