Tue Oct 11 06:02:18 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 06:02:18 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7060550 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): 25.70300 72.14200 ymin,ymax (A): -18.83100 31.59000 zmin,zma (A): 3.897000 46.35900 x,y,z range (A): 46.43900 50.42100 42.46200 scale (grids/A): 0.7060550 object centre (A): 48.92250 6.379500 25.12800 number of atom coordinates read : 2327 total number of charged atoms : 2002 net assigned charge : 6.500009 assigned positive charge : 325.3439 centred at (gu) : 89.26889 90.23833 90.33675 assigned negative charge : -318.8441 centred at (gu) : 89.39622 90.18970 90.41852 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7171 nv = 96 ne = 84 npr = 42805 no. pairs analyzed = 42805 no. exposed pairs = 2559 no. arc points = 17394 no. surface atoms = 879 nbur = 1448 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 484 mr = 4149 m= 1 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3409 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1641 ## 152 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8001 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.6612630E-08 1.2937949E-08 midg,1,midg; midg,igrid,midg 2.7561148E-08 7.9982009E-08 1,midg,midg; igrid,midg,midg 1.3183499E-07 -8.6596579E-09 gauss-seidel spectral radius is 0.9895465 estimated iterations to convergence 80 setup time was (sec) 0.3600000 now iterating at: 06:02:19 rms-change max change #iterations 0.1986655 30.77339 at 10iterations 2.4887765E-02 3.208735 at 20iterations 3.2041322E-03 0.4771326 at 30iterations 5.0198456E-04 6.4595222E-02 at 40iterations 1.1651588E-04 1.4869690E-02 at 50iterations finished qdiffx linear iterations at : 06:02:22 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.1651588E-04 1.4869690E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 06:02:23 3.370u 0.178s 0:04.43 79.9% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 06:02:23 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.118165 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): 25.70300 72.14200 ymin,ymax (A): -18.83100 31.59000 zmin,zma (A): 3.897000 46.35900 x,y,z range (A): 46.43900 50.42100 42.46200 scale (grids/A): 2.118165 object centre (A): 48.92250 6.379500 25.12800 number of atom coordinates read : 2327 total number of charged atoms : 2002 net assigned charge : 6.500009 assigned positive charge : 325.3439 centred at (gu) : 87.80647 90.71496 91.01020 assigned negative charge : -318.8441 centred at (gu) : 88.18848 90.56903 91.25566 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 76193 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17394 grid for indexing accessible points = 1.400000 m= 31175 mr = 54490 m= 6084 mr = 23818 m= 577 mr = 4186 m= 17 mr = 296 m= 0 mr = 9 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 31247 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 76 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 15883 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.7060550 object centre at (A) : 48.92250 6.379500 25.12800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0164596E-02 2.7952245E-02 midg,1,midg; midg,igrid,midg 4.6628825E-02 3.0079477E-02 1,midg,midg; igrid,midg,midg 4.3388091E-02 -4.4566691E-02 gauss-seidel spectral radius is 0.9988295 estimated iterations to convergence 231 setup time was (sec) 0.6200000 now iterating at: 06:02:23 rms-change max change #iterations 4.655270 193.6716 at 10iterations 2.301720 77.23190 at 20iterations 1.140501 35.67596 at 30iterations 0.5672312 18.30436 at 40iterations 0.2805435 9.356932 at 50iterations 0.1394584 4.285379 at 60iterations 6.9139056E-02 1.943888 at 70iterations 3.4377474E-02 1.091831 at 80iterations 1.7195765E-02 0.5461063 at 90iterations 8.5841138E-03 0.2791748 at 100iterations 4.2960811E-03 0.1300678 at 110iterations 2.1934523E-03 6.3920021E-02 at 120iterations finished qdiffx linear iterations at : 06:02:31 total time elapsed so far: 7.790000 # loops : 120 mean,max change (kT/e) : 2.1934523E-03 6.3920021E-02 energy calculations done at 7.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 06:02:32 7.936u 0.192s 0:09.01 90.1% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 06:02:32 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.177248 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): 25.70300 72.14200 ymin,ymax (A): -18.83100 31.59000 zmin,zma (A): 3.897000 46.35900 x,y,z range (A): 46.43900 50.42100 42.46200 scale (grids/A): 3.177248 object centre (A): 48.92250 6.379500 25.12800 number of atom coordinates read : 2327 total number of charged atoms : 2002 net assigned charge : 6.500009 assigned positive charge : 325.3439 centred at (gu) : 86.70976 91.07240 91.51531 assigned negative charge : -318.8441 centred at (gu) : 87.28283 90.85360 91.88343 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 175341 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17394 grid for indexing accessible points = 1.400000 m= 96841 mr = 130841 m= 39964 mr = 81185 m= 11608 mr = 33041 m= 2393 mr = 9143 m= 283 mr = 1756 m= 12 mr = 191 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.190000 number of dielectric boundary points 70285 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 16016 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 2.118165 object centre at (A) : 48.92250 6.379500 25.12800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1202754 0.2353236 midg,1,midg; midg,igrid,midg 0.3667043 0.1323778 1,midg,midg; igrid,midg,midg 0.4256299 -0.5549963 gauss-seidel spectral radius is 0.9992961 estimated iterations to convergence 297 setup time was (sec) 1.420000 now iterating at: 06:02:33 rms-change max change #iterations 10.39614 430.9038 at 10iterations 6.149052 144.2576 at 20iterations 3.636373 94.92770 at 30iterations 2.141900 41.14265 at 40iterations 1.260651 24.65791 at 50iterations 0.7424254 17.46768 at 60iterations 0.4358982 10.02634 at 70iterations 0.2551883 4.598433 at 80iterations 0.1497804 2.770405 at 90iterations 8.7758705E-02 1.528168 at 100iterations 5.1500630E-02 0.9903569 at 110iterations 3.0265054E-02 0.7048111 at 120iterations 1.7877862E-02 0.3194790 at 130iterations 1.0660299E-02 0.1891556 at 140iterations 6.4519919E-03 0.1105785 at 150iterations 3.9915172E-03 7.2885513E-02 at 160iterations 2.5690838E-03 5.3203583E-02 at 170iterations 1.7437532E-03 3.2306671E-02 at 180iterations finished qdiffx linear iterations at : 06:02:45 total time elapsed so far: 12.77000 # loops : 180 mean,max change (kT/e) : 1.7437532E-03 3.2306671E-02 energy calculations done at 12.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 06:02:46 12.907u 0.204s 0:14.18 92.3% 0+0k 0+0io 0pf+0w