Wed Feb 15 08:54:47 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:54:48 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 ! Automatically converted by prot2crg.py # of charge parameter records: 960 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1727 !!! WARNING: HIZ 132 has a net charge of 0.2000 !!! WARNING: HIZ 136 has a net charge of 0.2000 !!! WARNING: ZN4 490 has a net charge of 1.6000 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: 0.7381297 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): -51.99600 -3.766000 ymin,ymax (A): 3.052000 47.84600 zmin,zma (A): 42.25300 87.01000 x,y,z range (A): 48.23000 44.79400 44.75700 scale (grids/A): 0.7381297 object centre (A): -27.88100 25.44900 64.63150 number of atom coordinates read : 1727 total number of charged atoms : 1587 net assigned charge : -6.999991 assigned positive charge : 262.0143 centred at (gu) : 89.33454 90.98610 89.55514 assigned negative charge : -269.0143 centred at (gu) : 89.47717 90.96235 89.97975 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6434 nv = 96 ne = 84 npr = 36609 no. pairs analyzed = 36609 no. exposed pairs = 2374 no. arc points = 16748 no. surface atoms = 809 nbur = 918 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 461 mr = 3385 m= 4 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.2700000 number of dielectric boundary points 3435 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1335 ## 98 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6809 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3449302E-07 -4.4454316E-07 midg,1,midg; midg,igrid,midg -1.1689917E-07 -1.2028117E-07 1,midg,midg; igrid,midg,midg -4.2752482E-09 -2.1118086E-07 gauss-seidel spectral radius is 0.9903987 estimated iterations to convergence 83 setup time was (sec) 0.5100000 now iterating at: 08:54:48 rms-change max change #iterations 0.2271717 40.45612 at 10iterations 2.9728390E-02 4.565626 at 20iterations 3.9334125E-03 0.5344582 at 30iterations 5.2969670E-04 7.2006226E-02 at 40iterations 6.9062393E-05 9.5081329E-03 at 50iterations finished qdiffx linear iterations at : 08:54:51 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 6.9062393E-05 9.5081329E-03 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 08:54:55 3.318u 0.143s 0:07.67 44.9% 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 Wed Feb 15 2012 at 08:54:56 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 ! Automatically converted by prot2crg.py # of charge parameter records: 960 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1727 !!! WARNING: HIZ 132 has a net charge of 0.2000 !!! WARNING: HIZ 136 has a net charge of 0.2000 !!! WARNING: ZN4 490 has a net charge of 1.6000 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: 2.214389 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): -51.99600 -3.766000 ymin,ymax (A): 3.052000 47.84600 zmin,zma (A): 42.25300 87.01000 x,y,z range (A): 48.23000 44.79400 44.75700 scale (grids/A): 2.214389 object centre (A): -27.88100 25.44900 64.63150 number of atom coordinates read : 1727 total number of charged atoms : 1587 net assigned charge : -6.999991 assigned positive charge : 262.0143 centred at (gu) : 88.00394 92.95842 88.66547 assigned negative charge : -269.0143 centred at (gu) : 88.43172 92.88731 89.93965 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 66833 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16748 grid for indexing accessible points = 1.400000 m= 26792 mr = 44220 m= 5817 mr = 19924 m= 591 mr = 3967 m= 16 mr = 294 m= 0 mr = 2 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 465 time to turn everything in is 0.5700000 number of dielectric boundary points 31642 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 40 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 12631 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) : 0.7381297 object centre at (A) : -27.88100 25.44900 64.63150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2925654E-02 -0.1166089 midg,1,midg; midg,igrid,midg -6.8000063E-02 -7.2857305E-02 1,midg,midg; igrid,midg,midg 4.8383545E-02 -7.1029603E-02 gauss-seidel spectral radius is 0.9988880 estimated iterations to convergence 237 setup time was (sec) 0.8600000 now iterating at: 08:54:57 rms-change max change #iterations 4.687888 194.9674 at 10iterations 2.363160 90.71140 at 20iterations 1.186842 41.44850 at 30iterations 0.5982516 21.61069 at 40iterations 0.3015442 9.217110 at 50iterations 0.1520829 4.640528 at 60iterations 7.6830313E-02 2.437000 at 70iterations 3.8768478E-02 1.267296 at 80iterations 1.9501749E-02 0.5910168 at 90iterations 9.8286849E-03 0.3073475 at 100iterations 4.9545225E-03 0.1548939 at 110iterations 2.4976060E-03 7.7054977E-02 at 120iterations finished qdiffx linear iterations at : 08:55:04 total time elapsed so far: 7.440000 # loops : 120 mean,max change (kT/e) : 2.4976060E-03 7.7054977E-02 energy calculations done at 7.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 08:55:04 7.633u 0.236s 0:08.45 93.0% 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 Wed Feb 15 2012 at 08:55:04 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 ! Automatically converted by prot2crg.py # of charge parameter records: 960 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1727 !!! WARNING: HIZ 132 has a net charge of 0.2000 !!! WARNING: HIZ 136 has a net charge of 0.2000 !!! WARNING: ZN4 490 has a net charge of 1.6000 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: 3.321584 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): -51.99600 -3.766000 ymin,ymax (A): 3.052000 47.84600 zmin,zma (A): 42.25300 87.01000 x,y,z range (A): 48.23000 44.79400 44.75700 scale (grids/A): 3.321584 object centre (A): -27.88100 25.44900 64.63150 number of atom coordinates read : 1727 total number of charged atoms : 1587 net assigned charge : -6.999991 assigned positive charge : 262.0143 centred at (gu) : 87.00599 94.43769 87.99830 assigned negative charge : -269.0143 centred at (gu) : 87.64762 94.33109 89.90958 start vw surface at 0.1400000 fill in re-entrant regions at 0.7800000 boundary points on vw surface= 153686 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16748 grid for indexing accessible points = 1.400000 m= 80675 mr = 106885 m= 35311 mr = 65777 m= 11144 mr = 28958 m= 2386 mr = 8713 m= 300 mr = 1775 m= 8 mr = 203 m= 0 mr = 3 time to grow re-entrant surface = 0.8200001 no. cavity mid-points inaccessible to solvent = 1699 time to turn everything in is 1.720000 number of dielectric boundary points 71196 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.860000 number of grid points assigned charge 12696 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) : 2.214389 object centre at (A) : -27.88100 25.44900 64.63150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0918544E-02 -1.179490 midg,1,midg; midg,igrid,midg -0.4313386 -0.5937633 1,midg,midg; igrid,midg,midg 0.1018524 -1.191543 gauss-seidel spectral radius is 0.9993109 estimated iterations to convergence 301 setup time was (sec) 2.040000 now iterating at: 08:55:07 rms-change max change #iterations 10.19538 332.2042 at 10iterations 6.011512 130.9923 at 20iterations 3.537168 62.11938 at 30iterations 2.079245 39.97905 at 40iterations 1.218348 22.64211 at 50iterations 0.7153898 13.28065 at 60iterations 0.4188286 7.292610 at 70iterations 0.2451155 4.525704 at 80iterations 0.1438976 2.655598 at 90iterations 8.4006935E-02 1.500204 at 100iterations 4.9318403E-02 0.8931122 at 110iterations 2.8808644E-02 0.5546131 at 120iterations 1.6866649E-02 0.2937078 at 130iterations 9.8759513E-03 0.1783710 at 140iterations 5.7819951E-03 0.1087694 at 150iterations 3.3899499E-03 6.9104791E-02 at 160iterations 1.9861318E-03 3.3065796E-02 at 170iterations 1.1657381E-03 2.1034718E-02 at 180iterations finished qdiffx linear iterations at : 08:55:17 total time elapsed so far: 12.86000 # loops : 180 mean,max change (kT/e) : 1.1657381E-03 2.1034718E-02 energy calculations done at 12.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.04000 DelPhi exited at 08:55:18 13.042u 0.233s 0:13.60 97.5% 0+0k 0+0io 0pf+0w