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 - 13:00:03 PST
