Mani,
Can you email me the input file so we can see what's the cause?
Ray
On Mon, Feb 11, 2013 at 12:48 PM, manikanthan bhavaraju
<mhb75.msstate.edu> wrote:
> Jason,
>
> Thanks for replying.
>
> I have changed the inp to 1 and radiopt to 0 in the MMPBSA.py script in
> the Ambertools1.5 and ran the script. The pbsa input is showing the changed
> values but the script is still crashing while calculating pbsa
>
> Here is the error message
>
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using
> /home/srg/mhb75/Download/amber12/bin/mmpbsa_py_energy
> cpptraj found! Using /home/srg/mhb75/Download/amber12/bin/cpptraj
> Preparing trajectories for simulation...
> 10 frames were processed by cpptraj for use in calculation.
>
> Beginning GB calculations with
> /home/srg/mhb75/Download/amber12/bin/mmpbsa_py_energy
> calculating complex contribution...
> calculating receptor contribution...
> calculating ligand contribution...
>
> Beginning PB calculations with
> /home/srg/mhb75/Download/amber12/bin/mmpbsa_py_energy
> calculating complex contribution...
> CalcError: /home/srg/mhb75/Download/amber12/bin/mmpbsa_py_energy failed
> with prmtop hpon1_cpxn_near_imp.prmtop!
> Exiting. All files have been retained.
>
> here is the pbsa output file
>
> Reading parm file (hpon1_cpxn_near_imp.prmtop)
> title:
> default_name
>
> mm_options: e_debug=3
> mm_options: ipb=2
> mm_options: inp=1
> mm_options: epsin=1.000000
> mm_options: epsout=80.000000
> mm_options: smoothopt=1
> 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=0.557000
> mm_options: cavity_surften=0.037800
> mm_options: cavity_offset=-0.569200
> Processing ASCII trajectory (_MMPBSA_complex.mdcrd.0)
>
> Processing frame 1
> iter Total bad vdW elect nonpolar EPB
> frms
> _MMPBSA_complex_pb.mdout.0
>
> Can you provide me any further assistance?
>
> mani
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Received on Mon Feb 11 2013 - 13:30:04 PST
