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
> >
> > _______________________________________________
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> >
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Feb 07 2012 - 09:00:04 PST
