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
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Received on Tue Feb 07 2012 - 12:30:03 PST
