Mon Oct 10 18:36:40 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 18:36:40 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2205 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6827772 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): -41.79400 4.074000 ymin,ymax (A): 57.31500 106.8570 zmin,zma (A): -21.85300 30.28700 x,y,z range (A): 45.86800 49.54200 52.14000 scale (grids/A): 0.6827772 object centre (A): -18.86000 82.08600 4.216999 number of atom coordinates read : 2205 total number of charged atoms : 2069 net assigned charge : 2.500008 assigned positive charge : 329.0042 centred at (gu) : 89.49804 88.38710 88.27835 assigned negative charge : -326.5048 centred at (gu) : 89.46666 88.54147 88.16776 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7057 nv = 96 ne = 84 npr = 44227 no. pairs analyzed = 44227 no. exposed pairs = 2781 no. arc points = 19664 no. surface atoms = 937 nbur = 1268 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 454 mr = 3889 m= 1 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.1600000 number of dielectric boundary points 3542 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1789 ## 161 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7930 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.0627060E-08 3.0571172E-08 midg,1,midg; midg,igrid,midg 7.7428417E-08 -2.4468406E-08 1,midg,midg; igrid,midg,midg 2.3961058E-09 1.8538383E-08 gauss-seidel spectral radius is 0.9888461 estimated iterations to convergence 77 setup time was (sec) 0.3400000 now iterating at: 18:36:41 rms-change max change #iterations 0.1766010 23.12900 at 10iterations 1.9901045E-02 2.912066 at 20iterations 2.2710375E-03 0.3129563 at 30iterations 2.6146666E-04 3.6390305E-02 at 40iterations 3.0672181E-05 4.3830872E-03 at 50iterations finished qdiffx linear iterations at : 18:36:43 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 3.0672181E-05 4.3830872E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 18:36:44 3.327u 0.182s 0:03.80 92.1% 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 Mon Oct 10 2011 at 18:36:44 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2205 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: 2.048331 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): -41.79400 4.074000 ymin,ymax (A): 57.31500 106.8570 zmin,zma (A): -21.85300 30.28700 x,y,z range (A): 45.86800 49.54200 52.14000 scale (grids/A): 2.048331 object centre (A): -18.86000 82.08600 4.216999 number of atom coordinates read : 2205 total number of charged atoms : 2069 net assigned charge : 2.500008 assigned positive charge : 329.0042 centred at (gu) : 88.49377 85.16080 84.83460 assigned negative charge : -326.5048 centred at (gu) : 88.39993 85.62419 84.50290 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 74505 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19664 grid for indexing accessible points = 1.400000 m= 28751 mr = 51216 m= 5440 mr = 21567 m= 456 mr = 3620 m= 10 mr = 228 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 525 time to turn everything in is 0.3700000 number of dielectric boundary points 32531 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 95 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 16415 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) : 0.6827772 object centre at (A) : -18.86000 82.08600 4.216999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7952319E-02 4.7454707E-02 midg,1,midg; midg,igrid,midg 4.6630070E-02 -1.3918245E-02 1,midg,midg; igrid,midg,midg 1.0302559E-02 1.4049450E-02 gauss-seidel spectral radius is 0.9987763 estimated iterations to convergence 226 setup time was (sec) 0.5900000 now iterating at: 18:36:45 rms-change max change #iterations 4.468270 258.7943 at 10iterations 2.170116 75.93772 at 20iterations 1.058358 30.87448 at 30iterations 0.5157592 15.70411 at 40iterations 0.2509571 7.973150 at 50iterations 0.1229370 3.913693 at 60iterations 5.9705030E-02 1.716911 at 70iterations 2.9143499E-02 0.8488741 at 80iterations 1.4209309E-02 0.4230719 at 90iterations 6.9340104E-03 0.2243299 at 100iterations 3.3816763E-03 0.1126468 at 110iterations 1.6516985E-03 5.1809311E-02 at 120iterations finished qdiffx linear iterations at : 18:36:52 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 1.6516985E-03 5.1809311E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 18:36:52 7.776u 0.174s 0:08.25 96.2% 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 18:36:52 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2205 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.072497 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): -41.79400 4.074000 ymin,ymax (A): 57.31500 106.8570 zmin,zma (A): -21.85300 30.28700 x,y,z range (A): 45.86800 49.54200 52.14000 scale (grids/A): 3.072497 object centre (A): -18.86000 82.08600 4.216999 number of atom coordinates read : 2205 total number of charged atoms : 2069 net assigned charge : 2.500008 assigned positive charge : 329.0042 centred at (gu) : 87.74034 82.74114 82.25183 assigned negative charge : -326.5048 centred at (gu) : 87.59987 83.43633 81.75435 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 172034 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19664 grid for indexing accessible points = 1.400000 m= 89114 mr = 123886 m= 36621 mr = 73193 m= 10158 mr = 30079 m= 1840 mr = 7877 m= 193 mr = 1385 m= 8 mr = 129 m= 0 mr = 3 time to grow re-entrant surface = 0.5700000 no. cavity mid-points inaccessible to solvent = 1726 time to turn everything in is 0.9800000 number of dielectric boundary points 73416 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 16552 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) : 2.048331 object centre at (A) : -18.86000 82.08600 4.216999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6015376E-02 0.9001226 midg,1,midg; midg,igrid,midg 0.3926544 -2.8445352E-02 1,midg,midg; igrid,midg,midg 0.1458374 5.2660901E-02 gauss-seidel spectral radius is 0.9992878 estimated iterations to convergence 296 setup time was (sec) 1.210000 now iterating at: 18:36:54 rms-change max change #iterations 10.25820 384.6774 at 10iterations 6.055634 120.7737 at 20iterations 3.565736 66.68768 at 30iterations 2.089590 41.18254 at 40iterations 1.225061 24.81634 at 50iterations 0.7148670 12.43125 at 60iterations 0.4170386 7.007316 at 70iterations 0.2425615 4.504370 at 80iterations 0.1414677 2.653555 at 90iterations 8.2082585E-02 1.467326 at 100iterations 4.7684412E-02 0.8264999 at 110iterations 2.7780036E-02 0.4545708 at 120iterations 1.6163664E-02 0.2756424 at 130iterations 9.3757734E-03 0.1581306 at 140iterations 5.4509356E-03 9.4249725E-02 at 150iterations 3.1646488E-03 5.1380157E-02 at 160iterations 1.8380536E-03 3.0456305E-02 at 170iterations 1.0691528E-03 1.7482758E-02 at 180iterations finished qdiffx linear iterations at : 18:37:05 total time elapsed so far: 12.50000 # loops : 180 mean,max change (kT/e) : 1.0691528E-03 1.7482758E-02 energy calculations done at 12.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.64000 DelPhi exited at 18:37:05 12.638u 0.226s 0:13.15 97.7% 0+0k 0+0io 0pf+0w