Tue Oct 11 05:17:54 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+sph2.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 = amb2.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 05:17:54 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: MG5 580 has a net charge of 1.4000 !!! WARNING: ZN5 581 has a net charge of 1.4000 !!! WARNING: ZN5 582 has a net charge of 1.4000 !!! WARNING: ZN5 583 has a net charge of 1.4000 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: 0.6892279 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): 15.66400 62.96400 ymin,ymax (A): -3.632000 34.14100 zmin,zma (A): 20.07800 71.73000 x,y,z range (A): 47.30000 37.77300 51.65200 scale (grids/A): 0.6892279 object centre (A): 39.31400 15.25450 45.90400 number of atom coordinates read : 2327 total number of charged atoms : 2001 net assigned charge : 11.32501 assigned positive charge : 331.0309 centred at (gu) : 91.50873 89.54582 89.11293 assigned negative charge : -319.7061 centred at (gu) : 91.58887 89.48506 89.00556 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6812 nv = 96 ne = 84 npr = 42669 no. pairs analyzed = 42669 no. exposed pairs = 2604 no. arc points = 17656 no. surface atoms = 889 nbur = 1438 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 452 mr = 3938 m= 4 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3246 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1693 ## 183 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7698 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0519406E-08 8.1979017E-08 midg,1,midg; midg,igrid,midg 4.5579426E-08 7.5315022E-08 1,midg,midg; igrid,midg,midg 6.6115035E-08 4.6700009E-08 gauss-seidel spectral radius is 0.9890357 estimated iterations to convergence 78 setup time was (sec) 0.3700000 now iterating at: 05:17:54 rms-change max change #iterations 0.1912188 27.21019 at 10iterations 2.2034610E-02 3.195343 at 20iterations 2.6431666E-03 0.3792953 at 30iterations 3.1392547E-04 3.8904190E-02 at 40iterations 3.9374067E-05 5.2909851E-03 at 50iterations finished qdiffx linear iterations at : 05:17:57 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 3.9374067E-05 5.2909851E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 05:17:58 3.392u 0.161s 0:03.94 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 05:17:58 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: MG5 580 has a net charge of 1.4000 !!! WARNING: ZN5 581 has a net charge of 1.4000 !!! WARNING: ZN5 582 has a net charge of 1.4000 !!! WARNING: ZN5 583 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.067683 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): 15.66400 62.96400 ymin,ymax (A): -3.632000 34.14100 zmin,zma (A): 20.07800 71.73000 x,y,z range (A): 47.30000 37.77300 51.65200 scale (grids/A): 2.067683 object centre (A): 39.31400 15.25450 45.90400 number of atom coordinates read : 2327 total number of charged atoms : 2001 net assigned charge : 11.32501 assigned positive charge : 331.0309 centred at (gu) : 94.52627 88.63738 87.33863 assigned negative charge : -319.7061 centred at (gu) : 94.76668 88.45526 87.01663 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 72566 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17656 grid for indexing accessible points = 1.400000 m= 29124 mr = 51662 m= 5476 mr = 22147 m= 453 mr = 3699 m= 12 mr = 222 m= 0 mr = 2 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 138 time to turn everything in is 0.3800000 number of dielectric boundary points 29899 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 82 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 15845 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) : 0.6892279 object centre at (A) : 39.31400 15.25450 45.90400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7561511E-02 5.4148659E-02 midg,1,midg; midg,igrid,midg 2.9217120E-02 4.3261461E-02 1,midg,midg; igrid,midg,midg 2.6857292E-02 3.7415434E-02 gauss-seidel spectral radius is 0.9987799 estimated iterations to convergence 227 setup time was (sec) 0.6000000 now iterating at: 05:17:59 rms-change max change #iterations 4.503384 196.1092 at 10iterations 2.207734 79.46513 at 20iterations 1.071184 32.72560 at 30iterations 0.5246184 16.06832 at 40iterations 0.2560605 8.215656 at 50iterations 0.1254772 3.646341 at 60iterations 6.1556716E-02 1.881016 at 70iterations 2.9981004E-02 0.9433365 at 80iterations 1.4645897E-02 0.4665756 at 90iterations 7.1736262E-03 0.2214108 at 100iterations 3.5075587E-03 0.1100945 at 110iterations 1.7143068E-03 5.7687759E-02 at 120iterations finished qdiffx linear iterations at : 05:18:06 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 1.7143068E-03 5.7687759E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 05:18:07 7.911u 0.176s 0:08.65 93.4% 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 05:18:07 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: MG5 580 has a net charge of 1.4000 !!! WARNING: ZN5 581 has a net charge of 1.4000 !!! WARNING: ZN5 582 has a net charge of 1.4000 !!! WARNING: ZN5 583 has a net charge of 1.4000 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: 3.101525 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): 15.66400 62.96400 ymin,ymax (A): -3.632000 34.14100 zmin,zma (A): 20.07800 71.73000 x,y,z range (A): 47.30000 37.77300 51.65200 scale (grids/A): 3.101525 object centre (A): 39.31400 15.25450 45.90400 number of atom coordinates read : 2327 total number of charged atoms : 2001 net assigned charge : 11.32501 assigned positive charge : 331.0309 centred at (gu) : 96.78922 87.95608 86.00792 assigned negative charge : -319.7061 centred at (gu) : 97.14993 87.68291 85.52499 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 167302 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17656 grid for indexing accessible points = 1.400000 m= 90758 mr = 124163 m= 36596 mr = 75706 m= 10352 mr = 30178 m= 1911 mr = 8085 m= 184 mr = 1414 m= 3 mr = 93 m= 0 mr = 2 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 570 time to turn everything in is 1.110000 number of dielectric boundary points 67465 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 16007 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) : 2.067683 object centre at (A) : 39.31400 15.25450 45.90400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4380916 0.4156127 midg,1,midg; midg,igrid,midg 0.2515547 0.3840567 1,midg,midg; igrid,midg,midg 0.2226752 0.5621791 gauss-seidel spectral radius is 0.9992835 estimated iterations to convergence 295 setup time was (sec) 1.340000 now iterating at: 05:18:08 rms-change max change #iterations 10.19805 380.0699 at 10iterations 6.010489 132.6786 at 20iterations 3.527864 87.94202 at 30iterations 2.071979 40.03304 at 40iterations 1.213001 25.65163 at 50iterations 0.7109619 17.40122 at 60iterations 0.4153062 7.742157 at 70iterations 0.2425631 5.653683 at 80iterations 0.1413644 2.713982 at 90iterations 8.2341641E-02 1.741940 at 100iterations 4.8033599E-02 0.9797010 at 110iterations 2.8017020E-02 0.5452232 at 120iterations 1.6321525E-02 0.3008137 at 130iterations 9.5601417E-03 0.1632462 at 140iterations 5.6070606E-03 9.8142624E-02 at 150iterations 3.3032468E-03 6.3997447E-02 at 160iterations 1.9707542E-03 4.0420532E-02 at 170iterations 1.1995053E-03 2.4299622E-02 at 180iterations finished qdiffx linear iterations at : 05:18:19 total time elapsed so far: 12.57000 # loops : 180 mean,max change (kT/e) : 1.1995053E-03 2.4299622E-02 energy calculations done at 12.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.71000 DelPhi exited at 05:18:20 12.711u 0.206s 0:13.19 97.8% 0+0k 0+0io 0pf+0w