Tue Oct 11 04:42:27 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 04:42:27 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2730 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: 0.6536428 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): -12.83200 36.33200 ymin,ymax (A): -25.81900 22.78800 zmin,zma (A): -9.263000 45.20100 x,y,z range (A): 49.16400 48.60700 54.46400 scale (grids/A): 0.6536428 object centre (A): 11.75000 -1.515500 17.96900 number of atom coordinates read : 2730 total number of charged atoms : 2582 net assigned charge : 3.500013 assigned positive charge : 413.5267 centred at (gu) : 90.70383 90.47405 91.76400 assigned negative charge : -410.0273 centred at (gu) : 90.44696 90.28641 91.71060 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7586 nv = 96 ne = 84 npr = 56808 no. pairs analyzed = 56808 no. exposed pairs = 3219 no. arc points = 22268 no. surface atoms = 1093 nbur = 1637 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 404 mr = 4290 m= 1 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.2300000 number of dielectric boundary points 3646 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2246 ## 224 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9272 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7258617E-09 2.3531635E-08 midg,1,midg; midg,igrid,midg -2.4374714E-08 4.3513236E-08 1,midg,midg; igrid,midg,midg -3.4235189E-08 5.9272260E-08 gauss-seidel spectral radius is 0.9878749 estimated iterations to convergence 74 setup time was (sec) 0.4100000 now iterating at: 04:42:28 rms-change max change #iterations 0.1595597 21.95759 at 10iterations 1.7024074E-02 2.540731 at 20iterations 1.7637538E-03 0.2704849 at 30iterations 1.9140678E-04 2.6596069E-02 at 40iterations 2.3026243E-05 2.9942989E-03 at 50iterations finished qdiffx linear iterations at : 04:42:30 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 2.3026243E-05 2.9942989E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 04:42:31 3.451u 0.166s 0:04.35 82.9% 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 04:42:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2730 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: 1.960928 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): -12.83200 36.33200 ymin,ymax (A): -25.81900 22.78800 zmin,zma (A): -9.263000 45.20100 x,y,z range (A): 49.16400 48.60700 54.46400 scale (grids/A): 1.960928 object centre (A): 11.75000 -1.515500 17.96900 number of atom coordinates read : 2730 total number of charged atoms : 2582 net assigned charge : 3.500013 assigned positive charge : 413.5267 centred at (gu) : 92.11080 91.42149 95.29121 assigned negative charge : -410.0273 centred at (gu) : 91.34053 90.85887 95.13159 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 81487 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22268 grid for indexing accessible points = 1.400000 m= 30166 mr = 57451 m= 4777 mr = 22492 m= 315 mr = 3111 m= 5 mr = 118 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1777 time to turn everything in is 0.4100000 number of dielectric boundary points 33578 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 136 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 20362 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) : 0.6536428 object centre at (A) : 11.75000 -1.515500 17.96900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3587437E-02 4.0142345E-03 midg,1,midg; midg,igrid,midg -1.8729001E-02 3.1543281E-02 1,midg,midg; igrid,midg,midg -6.5089259E-03 7.1193859E-02 gauss-seidel spectral radius is 0.9987150 estimated iterations to convergence 221 setup time was (sec) 0.6400000 now iterating at: 04:42:32 rms-change max change #iterations 4.627810 194.2549 at 10iterations 2.213525 71.09509 at 20iterations 1.062133 33.26566 at 30iterations 0.5090651 14.43260 at 40iterations 0.2450340 7.001883 at 50iterations 0.1175918 3.441095 at 60iterations 5.6255542E-02 1.872463 at 70iterations 2.6934791E-02 0.7867508 at 80iterations 1.2951559E-02 0.3986918 at 90iterations 6.2345797E-03 0.1789856 at 100iterations 2.9844001E-03 9.4238281E-02 at 110iterations 1.4274525E-03 4.1833878E-02 at 120iterations finished qdiffx linear iterations at : 04:42:39 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 1.4274525E-03 4.1833878E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 04:42:40 7.967u 0.189s 0:08.90 91.4% 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 04:42:40 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2730 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: 2.941392 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): -12.83200 36.33200 ymin,ymax (A): -25.81900 22.78800 zmin,zma (A): -9.263000 45.20100 x,y,z range (A): 49.16400 48.60700 54.46400 scale (grids/A): 2.941392 object centre (A): 11.75000 -1.515500 17.96900 number of atom coordinates read : 2730 total number of charged atoms : 2582 net assigned charge : 3.500013 assigned positive charge : 413.5267 centred at (gu) : 93.16604 92.13220 97.93677 assigned negative charge : -410.0273 centred at (gu) : 92.01077 91.28835 97.69748 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 188116 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22268 grid for indexing accessible points = 1.400000 m= 96760 mr = 138441 m= 35705 mr = 79963 m= 8901 mr = 29113 m= 1323 mr = 6823 m= 111 mr = 884 m= 0 mr = 58 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 6269 time to turn everything in is 1.080000 number of dielectric boundary points 75634 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 20647 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) : 1.960928 object centre at (A) : 11.75000 -1.515500 17.96900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4435073 0.2075009 midg,1,midg; midg,igrid,midg -0.1831912 0.3497206 1,midg,midg; igrid,midg,midg -3.0852824E-02 0.5754461 gauss-seidel spectral radius is 0.9992741 estimated iterations to convergence 293 setup time was (sec) 1.310000 now iterating at: 04:42:42 rms-change max change #iterations 10.64560 416.6893 at 10iterations 6.236605 131.3215 at 20iterations 3.649858 70.88011 at 30iterations 2.125713 38.43597 at 40iterations 1.239814 27.02359 at 50iterations 0.7202189 13.89916 at 60iterations 0.4178357 6.977631 at 70iterations 0.2420412 4.458275 at 80iterations 0.1405172 2.646206 at 90iterations 8.1359990E-02 1.498399 at 100iterations 4.7196977E-02 0.7855356 at 110iterations 2.7290765E-02 0.4796906 at 120iterations 1.5793290E-02 0.2777481 at 130iterations 9.1370596E-03 0.1565199 at 140iterations 5.2952995E-03 9.8974228E-02 at 150iterations 3.0821704E-03 5.1730156E-02 at 160iterations 1.7926771E-03 3.0716896E-02 at 170iterations 1.0447316E-03 1.8245697E-02 at 180iterations finished qdiffx linear iterations at : 04:42:53 total time elapsed so far: 12.70000 # loops : 180 mean,max change (kT/e) : 1.0447316E-03 1.8245697E-02 energy calculations done at 12.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.82000 DelPhi exited at 04:42:54 12.826u 0.209s 0:13.50 96.4% 0+0k 0+0io 0pf+0w