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
Received on Sun Aug 14 2011 - 05:00:03 PDT
