Mon Oct 10 11:46:11 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 Mon Oct 10 2011 at 11:46:12 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: 233 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2105 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7406329 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): -20.61200 23.99100 ymin,ymax (A): -8.013000 37.56500 zmin,zma (A): -3.522000 44.54500 x,y,z range (A): 44.60300 45.57800 48.06700 scale (grids/A): 0.7406329 object centre (A): 1.689500 14.77600 20.51150 number of atom coordinates read : 2105 total number of charged atoms : 1967 net assigned charge : -4.999990 assigned positive charge : 315.6119 centred at (gu) : 88.91721 89.88300 89.98360 assigned negative charge : -320.6120 centred at (gu) : 88.93158 89.94273 90.12678 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7951 nv = 96 ne = 84 npr = 43473 no. pairs analyzed = 43473 no. exposed pairs = 2633 no. arc points = 19024 no. surface atoms = 892 nbur = 1213 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 545 mr = 4423 m= 6 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 98 time to turn everything in is 0.2800000 number of dielectric boundary points 3954 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1572 ## 142 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8389 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.6268231E-08 -2.3823661E-07 midg,1,midg; midg,igrid,midg -2.8754373E-08 -1.4807212E-07 1,midg,midg; igrid,midg,midg -9.0581679E-08 -8.5736559E-08 gauss-seidel spectral radius is 0.9904990 estimated iterations to convergence 83 setup time was (sec) 0.5000000 now iterating at: 11:46:12 rms-change max change #iterations 0.2486374 35.55661 at 10iterations 3.3809815E-02 4.211037 at 20iterations 4.5977049E-03 0.5590916 at 30iterations 6.1004492E-04 8.4299088E-02 at 40iterations 8.1818915E-05 1.0043144E-02 at 50iterations finished qdiffx linear iterations at : 11:46:15 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 8.1818915E-05 1.0043144E-02 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 11:46:15 3.464u 0.171s 0:03.95 91.8% 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 Mon Oct 10 2011 at 11:46:16 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: 233 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2105 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.221899 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): -20.61200 23.99100 ymin,ymax (A): -8.013000 37.56500 zmin,zma (A): -3.522000 44.54500 x,y,z range (A): 44.60300 45.57800 48.06700 scale (grids/A): 2.221899 object centre (A): 1.689500 14.77600 20.51150 number of atom coordinates read : 2105 total number of charged atoms : 1967 net assigned charge : -4.999990 assigned positive charge : 315.6119 centred at (gu) : 86.75160 89.64882 89.95074 assigned negative charge : -320.6120 centred at (gu) : 86.79459 89.82821 90.38039 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 83304 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19024 grid for indexing accessible points = 1.400000 m= 33384 mr = 57466 m= 7433 mr = 25584 m= 840 mr = 5189 m= 33 mr = 503 m= 0 mr = 11 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 2467 time to turn everything in is 0.6300000 number of dielectric boundary points 36241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 68 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 15678 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) : 0.7406329 object centre at (A) : 1.689500 14.77600 20.51150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2876337E-03 -0.1188918 midg,1,midg; midg,igrid,midg -2.4421969E-02 -3.3136807E-02 1,midg,midg; igrid,midg,midg -2.1959756E-02 -2.8693120E-03 gauss-seidel spectral radius is 0.9989262 estimated iterations to convergence 241 setup time was (sec) 0.9200000 now iterating at: 11:46:17 rms-change max change #iterations 5.088796 214.4775 at 10iterations 2.582747 89.72646 at 20iterations 1.312867 36.55733 at 30iterations 0.6701443 21.43517 at 40iterations 0.3409907 9.461550 at 50iterations 0.1736008 5.283598 at 60iterations 8.8821948E-02 2.361320 at 70iterations 4.5157965E-02 1.250591 at 80iterations 2.3087075E-02 0.6632614 at 90iterations 1.1741024E-02 0.3480854 at 100iterations 6.0031256E-03 0.2026539 at 110iterations 3.0516037E-03 8.6076736E-02 at 120iterations finished qdiffx linear iterations at : 11:46:23 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 3.0516037E-03 8.6076736E-02 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.710000 DelPhi exited at 11:46:24 7.714u 0.199s 0:08.24 95.8% 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 Mon Oct 10 2011 at 11:46:24 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: 233 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2105 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.332848 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): -20.61200 23.99100 ymin,ymax (A): -8.013000 37.56500 zmin,zma (A): -3.522000 44.54500 x,y,z range (A): 44.60300 45.57800 48.06700 scale (grids/A): 3.332848 object centre (A): 1.689500 14.77600 20.51150 number of atom coordinates read : 2105 total number of charged atoms : 1967 net assigned charge : -4.999990 assigned positive charge : 315.6119 centred at (gu) : 85.12743 89.47324 89.92612 assigned negative charge : -320.6120 centred at (gu) : 85.19180 89.74229 90.57059 start vw surface at 0.1400000 fill in re-entrant regions at 0.9200000 boundary points on vw surface= 191793 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19024 grid for indexing accessible points = 1.400000 m= 102160 mr = 138286 m= 44038 mr = 85045 m= 14312 mr = 36596 m= 3461 mr = 11552 m= 563 mr = 2688 m= 40 mr = 423 m= 0 mr = 17 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 8011 time to turn everything in is 2.040000 number of dielectric boundary points 81760 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.170000 number of grid points assigned charge 15736 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) : 2.221899 object centre at (A) : 1.689500 14.77600 20.51150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7619532E-02 -1.323851 midg,1,midg; midg,igrid,midg -0.2336013 -0.1726042 1,midg,midg; igrid,midg,midg -0.2831364 -8.8934578E-02 gauss-seidel spectral radius is 0.9993178 estimated iterations to convergence 302 setup time was (sec) 2.350000 now iterating at: 11:46:26 rms-change max change #iterations 10.95461 324.6100 at 10iterations 6.464467 123.0180 at 20iterations 3.812509 74.34564 at 30iterations 2.244402 37.67645 at 40iterations 1.319753 21.93745 at 50iterations 0.7779137 12.91803 at 60iterations 0.4566947 8.250378 at 70iterations 0.2688477 4.555050 at 80iterations 0.1577618 2.609640 at 90iterations 9.2640840E-02 1.499084 at 100iterations 5.4443967E-02 0.8287849 at 110iterations 3.1957317E-02 0.5233483 at 120iterations 1.8771984E-02 0.3092594 at 130iterations 1.1010211E-02 0.1726627 at 140iterations 6.4540128E-03 9.7538233E-02 at 150iterations 3.7935316E-03 5.9382915E-02 at 160iterations 2.2251687E-03 3.7264824E-02 at 170iterations 1.3060875E-03 1.9689560E-02 at 180iterations finished qdiffx linear iterations at : 11:46:37 total time elapsed so far: 12.85000 # loops : 180 mean,max change (kT/e) : 1.3060875E-03 1.9689560E-02 energy calculations done at 12.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.07000 DelPhi exited at 11:46:37 13.072u 0.219s 0:13.57 97.8% 0+0k 0+0io 0pf+0w