Sat Oct 8 20:55:07 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 Sat Oct 8 2011 at 20:55:07 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2524 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 435 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: 0.6461332 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): -32.10100 17.58700 ymin,ymax (A): -23.19900 23.44200 zmin,zma (A): -12.63300 42.46400 x,y,z range (A): 49.68800 46.64100 55.09700 scale (grids/A): 0.6461332 object centre (A): -7.256999 0.1215000 14.91550 number of atom coordinates read : 2524 total number of charged atoms : 2384 net assigned charge : 2.500009 assigned positive charge : 379.8112 centred at (gu) : 88.66319 89.11780 90.23862 assigned negative charge : -377.3116 centred at (gu) : 88.54021 89.14503 90.16208 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6994 nv = 96 ne = 84 npr = 52640 no. pairs analyzed = 52640 no. exposed pairs = 2952 no. arc points = 21094 no. surface atoms = 987 nbur = 1537 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 376 mr = 3971 m= 4 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 125 time to turn everything in is 0.1900000 number of dielectric boundary points 3362 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2038 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8400 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4761657E-09 1.5416987E-08 midg,1,midg; midg,igrid,midg 9.8149648E-09 7.6170392E-10 1,midg,midg; igrid,midg,midg -1.6312846E-08 1.5602081E-08 gauss-seidel spectral radius is 0.9875793 estimated iterations to convergence 73 setup time was (sec) 0.4100000 now iterating at: 20:55:08 rms-change max change #iterations 0.1506090 30.41879 at 10iterations 1.5381501E-02 2.154673 at 20iterations 1.5729264E-03 0.2320938 at 30iterations 1.6718845E-04 2.2396088E-02 at 40iterations 1.8436471E-05 2.7389526E-03 at 50iterations finished qdiffx linear iterations at : 20:55:11 total time elapsed so far: 3.530000 # loops : 50 mean,max change (kT/e) : 1.8436471E-05 2.7389526E-03 energy calculations done at 3.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.660000 DelPhi exited at 20:55:12 3.664u 0.216s 0:04.17 92.8% 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 Sat Oct 8 2011 at 20:55:12 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2524 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 435 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: 1.938400 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): -32.10100 17.58700 ymin,ymax (A): -23.19900 23.44200 zmin,zma (A): -12.63300 42.46400 x,y,z range (A): 49.68800 46.64100 55.09700 scale (grids/A): 1.938400 object centre (A): -7.256999 0.1215000 14.91550 number of atom coordinates read : 2524 total number of charged atoms : 2384 net assigned charge : 2.500009 assigned positive charge : 379.8112 centred at (gu) : 85.98904 87.35280 90.71556 assigned negative charge : -377.3116 centred at (gu) : 85.62048 87.43495 90.48618 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 75390 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21094 grid for indexing accessible points = 1.400000 m= 27636 mr = 53179 m= 4323 mr = 20666 m= 220 mr = 2731 m= 4 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 3349 time to turn everything in is 0.3900000 number of dielectric boundary points 30942 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 108 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 18790 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) : 0.6461332 object centre at (A) : -7.256999 0.1215000 14.91550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2281978E-02 -3.3684904E-03 midg,1,midg; midg,igrid,midg 1.4220702E-02 -2.0338080E-03 1,midg,midg; igrid,midg,midg -4.7374894E-03 4.3537427E-02 gauss-seidel spectral radius is 0.9986728 estimated iterations to convergence 217 setup time was (sec) 0.6200000 now iterating at: 20:55:13 rms-change max change #iterations 4.290042 189.8238 at 10iterations 2.032410 68.32041 at 20iterations 0.9627144 33.09435 at 30iterations 0.4572430 14.01586 at 40iterations 0.2168408 6.767075 at 50iterations 0.1028489 3.096958 at 60iterations 4.8626121E-02 1.515903 at 70iterations 2.3011703E-02 0.7612476 at 80iterations 1.0900873E-02 0.3530388 at 90iterations 5.1570199E-03 0.1750507 at 100iterations 2.4484319E-03 8.3557129E-02 at 110iterations 1.1598676E-03 4.3609619E-02 at 120iterations finished qdiffx linear iterations at : 20:55:20 total time elapsed so far: 8.270000 # loops : 120 mean,max change (kT/e) : 1.1598676E-03 4.3609619E-02 energy calculations done at 8.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.400000 DelPhi exited at 20:55:21 8.403u 0.238s 0:08.91 96.8% 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 Sat Oct 8 2011 at 20:55:21 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2524 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 435 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: 2.907599 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): -32.10100 17.58700 ymin,ymax (A): -23.19900 23.44200 zmin,zma (A): -12.63300 42.46400 x,y,z range (A): 49.68800 46.64100 55.09700 scale (grids/A): 2.907599 object centre (A): -7.256999 0.1215000 14.91550 number of atom coordinates read : 2524 total number of charged atoms : 2384 net assigned charge : 2.500009 assigned positive charge : 379.8112 centred at (gu) : 83.98341 86.02894 91.07317 assigned negative charge : -377.3116 centred at (gu) : 83.43064 86.15242 90.72936 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 174362 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21094 grid for indexing accessible points = 1.400000 m= 89113 mr = 128312 m= 32457 mr = 73824 m= 7884 mr = 26402 m= 986 mr = 5919 m= 49 mr = 612 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.5599999 no. cavity mid-points inaccessible to solvent = 11116 time to turn everything in is 0.9800000 number of dielectric boundary points 69763 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 19071 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) : 1.938400 object centre at (A) : -7.256999 0.1215000 14.91550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1141673 -2.5879014E-02 midg,1,midg; midg,igrid,midg 0.1387772 -6.3043267E-02 1,midg,midg; igrid,midg,midg 2.2628153E-02 0.5127585 gauss-seidel spectral radius is 0.9992610 estimated iterations to convergence 290 setup time was (sec) 1.240000 now iterating at: 20:55:22 rms-change max change #iterations 9.947669 481.5416 at 10iterations 5.785542 163.2150 at 20iterations 3.348839 80.36120 at 30iterations 1.937976 39.05641 at 40iterations 1.120276 21.80473 at 50iterations 0.6479737 12.40387 at 60iterations 0.3729666 7.505175 at 70iterations 0.2148101 4.014849 at 80iterations 0.1236683 2.427067 at 90iterations 7.1317390E-02 1.289068 at 100iterations 4.1119669E-02 0.8450470 at 110iterations 2.3681365E-02 0.4510803 at 120iterations 1.3636493E-02 0.2336922 at 130iterations 7.8712320E-03 0.1416454 at 140iterations 4.5518568E-03 8.1487656E-02 at 150iterations 2.6421403E-03 4.9194336E-02 at 160iterations 1.5450901E-03 3.0956268E-02 at 170iterations 9.0882875E-04 1.7784119E-02 at 180iterations finished qdiffx linear iterations at : 20:55:34 total time elapsed so far: 13.39000 # loops : 180 mean,max change (kT/e) : 9.0882875E-04 1.7784119E-02 energy calculations done at 13.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.53000 DelPhi exited at 20:55:35 13.529u 0.251s 0:14.07 97.8% 0+0k 0+0io 0pf+0w