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
Received on Sun Aug 14 2011 - 07:30:03 PDT
