I will look into this.
On Sun, Aug 14, 2011 at 8:12 PM, Hiromichi Tsurui <tsurui.juntendo.ac.jp>wrote:
> Thank you Jason.
> I directly used 4 prmtop files and 1 mdcrd file from ras-raf_top_mdcrd.tgz.
>
>
> >I don't see any error messages actually printed out by the program (the
> > mmpbsa_py_energy program, not MMPBSA), so it's hard to assess what went
> > wrong.
> >
> > Did you make any changes to any of the files from the tutorial before
> > running it?
> >
> > Thanks!
> > Jason
> >
> > On Sun, Aug 14, 2011 at 7:30 AM, HIromichi Tsurui
> > <tsurui.juntendo.ac.jp>wrote:
> >
> >> Hi all,
> >> I would like to calculate receptor-ligand interaction energy by
> >> MMPBSA/GBSA.
> >> I tried to do so using Tutorial Advanced 3, Ras-raf model. Energy
> >> calculation by GB seems to go well.
> >> However, mmpbsa_py_energy error occurred during PB calculations.
> >> Could anyone suggest me what happened and how should I do?
> >>
> >>
> >>
> >> $ MMPBSA -O -i mmpbsa_1b.in -o FINAL_RESULTS_MMPBSA.dat -sp
> >> ras-raf_solvated.prmtop -cp ras-raf.prmtop -rp ras.prmtop -lp
> >> raf.prmtop -y
> >> prod.mdcrd
> >> Reading command-line arguments and input files...
> >> Loading and checking parameter files for compatibility...
> >> ptraj found! Using /home/tsurui/Downloads/amber11/bin/ptraj
> >> mmpbsa_py_energy found! Using
> >> /home/tsurui/Downloads/amber11/bin/mmpbsa_py_energy for GB calculations
> >> mmpbsa_py_energy found! Using
> >> /home/tsurui/Downloads/amber11/bin/mmpbsa_py_energy for PB calculations
> >> Preparing trajectories for simulation...
> >> 50 frames were read in and processed by ptraj for use in calculation.
> >>
> >> Beginning GB calculations with mmpbsa_py_energy...
> >> calculating complex contribution...
> >> calculating receptor contribution...
> >> calculating ligand contribution...
> >>
> >> Beginning PB calculations with mmpbsa_py_energy...
> >> calculating complex contribution...
> >> PB Info in pb_read(): npopt has been overwritten with inp
> >> Error: mmpbsa_py_energy error during PB calculations!
> >> NOTE: All files have been retained for debugging purposes. Type
> MMPBSA.py
> >> --clean to erase these files.
> >>
> >>
> >> << _MMPBSA_complex_pb.mdout >>
> >> Reading parm file (ras-raf.prmtop)
> >> title:
> >>
> >> mm_options: e_debug=3
> >> mm_options: ipb=1
> >> mm_options: inp=1
> >> mm_options: epsin=1.000000
> >> mm_options: epsout=80.000000
> >> mm_options: smoothopt=0
> >> mm_options: istrng=100.000000
> >> mm_options: radiopt=0
> >> mm_options: dprob=1.400000
> >> mm_options: iprob=2.000000
> >> mm_options: npbopt=0
> >> mm_options: solvopt=1
> >> mm_options: accept=0.001000
> >> mm_options: maxitn=1000
> >> mm_options: fillratio=4.000000
> >> mm_options: space=0.500000
> >> mm_options: nfocus=2
> >> mm_options: fscale=8
> >> mm_options: bcopt=5
> >> mm_options: eneopt=2
> >> mm_options: cutnb=0.000000
> >> mm_options: sprob=1.400000
> >> mm_options: cavity_surften=0.005420
> >> mm_options: cavity_offset=-1.008000
> >> Processing ASCII trajectory (_MMPBSA_complex.mdcrd)
> >>
> >> Processing frame 1
> >> iter Total bad vdW elect nonpolar EPB
> >> frms
> >>
> >>
> >>
> >> _______________________________________________
> >> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
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> 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 Fri Aug 26 2011 - 19:00:04 PDT
