Hi,
Thanks for the reply.. In the output files, after minimization of each
frame, it says convergence satisfied.
I am unable to attach the _MMPBSA_*_nm.out files with this mail due to the
larger file size...
I have attached the _MMPBSA_ligand_nm.out file with this mail.
I am very thankful for your response.
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
>
--
Thank you,
With regards,
B. Sangeetha
Ph.D Scholar,
Centre for Bioinformatics,
Pondicherry University,
Pondicherry,
India
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Received on Mon Jan 30 2012 - 20:30:02 PST
