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
>>
>>
>>
>> _______________________________________________
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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
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Sun Aug 14 2011 - 17:30:02 PDT
