Mon Oct 10 17:01:06 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 Mon Oct 10 2011 at 17:01:06 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 = 2803 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: 0.5752420 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): -30.84000 31.04700 ymin,ymax (A): -22.05200 24.79300 zmin,zma (A): -7.364000 38.42300 x,y,z range (A): 61.88700 46.84500 45.78700 scale (grids/A): 0.5752420 object centre (A): 0.1034994 1.370500 15.52950 number of atom coordinates read : 2803 total number of charged atoms : 2664 net assigned charge : -2.999966 assigned positive charge : 419.0322 centred at (gu) : 90.51418 90.39903 89.71281 assigned negative charge : -422.0334 centred at (gu) : 90.61108 90.25254 89.67010 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6059 nv = 96 ne = 84 npr = 56597 no. pairs analyzed = 56597 no. exposed pairs = 3696 no. arc points = 25569 no. surface atoms = 1242 nbur = 1561 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 243 mr = 3063 m= 0 mr = 15 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.3000000 number of dielectric boundary points 3224 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2615 ## 287 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7757 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4088245E-09 1.9117048E-10 midg,1,midg; midg,igrid,midg -2.9193730E-09 2.2219171E-09 1,midg,midg; igrid,midg,midg 1.0201077E-09 -2.5990943E-09 gauss-seidel spectral radius is 0.9843916 estimated iterations to convergence 66 setup time was (sec) 0.5200000 now iterating at: 17:01:06 rms-change max change #iterations 8.9808419E-02 16.55435 at 10iterations 6.8319188E-03 1.006219 at 20iterations 5.1355257E-04 7.9330444E-02 at 30iterations 4.0030918E-05 6.3276291E-03 at 40iterations 3.0906042E-06 5.3024292E-04 at 50iterations finished qdiffx linear iterations at : 17:01:09 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 3.0906042E-06 5.3024292E-04 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 17:01:11 3.136u 0.144s 0:04.91 66.5% 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 17:01:11 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 = 2803 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.725726 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): -30.84000 31.04700 ymin,ymax (A): -22.05200 24.79300 zmin,zma (A): -7.364000 38.42300 x,y,z range (A): 61.88700 46.84500 45.78700 scale (grids/A): 1.725726 object centre (A): 0.1034994 1.370500 15.52950 number of atom coordinates read : 2803 total number of charged atoms : 2664 net assigned charge : -2.999966 assigned positive charge : 419.0322 centred at (gu) : 91.54195 91.19654 89.13800 assigned negative charge : -422.0334 centred at (gu) : 91.83296 90.75724 89.00996 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 66550 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25569 grid for indexing accessible points = 1.400000 m= 20334 mr = 44525 m= 2188 mr = 13801 m= 61 mr = 1043 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 888 time to turn everything in is 0.4800000 number of dielectric boundary points 29763 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 240 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 20668 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) : 0.5752420 object centre at (A) : 0.1034994 1.370500 15.52950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8493682E-03 -3.8765399E-03 midg,1,midg; midg,igrid,midg -1.7208626E-02 1.3700373E-02 1,midg,midg; igrid,midg,midg 4.4148448E-03 -8.7576518E-03 gauss-seidel spectral radius is 0.9983629 estimated iterations to convergence 196 setup time was (sec) 0.7500000 now iterating at: 17:01:11 rms-change max change #iterations 3.632398 174.2520 at 10iterations 1.575994 68.17023 at 20iterations 0.6832522 23.16126 at 30iterations 0.2977683 11.31017 at 40iterations 0.1292904 4.797491 at 50iterations 5.6288831E-02 1.999102 at 60iterations 2.4569510E-02 0.8373737 at 70iterations 1.0681626E-02 0.3894663 at 80iterations 4.6662968E-03 0.1586227 at 90iterations 2.0248208E-03 7.0391655E-02 at 100iterations 8.8379928E-04 3.1822205E-02 at 110iterations 3.8527825E-04 1.3229370E-02 at 120iterations finished qdiffx linear iterations at : 17:01:18 total time elapsed so far: 7.220000 # loops : 120 mean,max change (kT/e) : 3.8527825E-04 1.3229370E-02 energy calculations done at 7.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.400000 DelPhi exited at 17:01:19 7.400u 0.167s 0:08.09 93.4% 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 Mon Oct 10 2011 at 17:01:19 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 = 2803 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: 2.588589 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): -30.84000 31.04700 ymin,ymax (A): -22.05200 24.79300 zmin,zma (A): -7.364000 38.42300 x,y,z range (A): 61.88700 46.84500 45.78700 scale (grids/A): 2.588589 object centre (A): 0.1034994 1.370500 15.52950 number of atom coordinates read : 2803 total number of charged atoms : 2664 net assigned charge : -2.999966 assigned positive charge : 419.0322 centred at (gu) : 92.31258 91.79444 88.70692 assigned negative charge : -422.0334 centred at (gu) : 92.74937 91.13577 88.51476 start vw surface at 0.1800000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 154861 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25569 grid for indexing accessible points = 1.400000 m= 69889 mr = 109495 m= 20393 mr = 54496 m= 3284 mr = 15185 m= 217 mr = 2111 m= 8 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 3205 time to turn everything in is 1.180000 number of dielectric boundary points 67274 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 21306 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) : 1.725726 object centre at (A) : 0.1034994 1.370500 15.52950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6848334E-02 -5.1913749E-02 midg,1,midg; midg,igrid,midg -0.1833889 0.2137452 1,midg,midg; igrid,midg,midg 0.3895320 -7.5506559E-03 gauss-seidel spectral radius is 0.9991908 estimated iterations to convergence 278 setup time was (sec) 1.490000 now iterating at: 17:01:21 rms-change max change #iterations 9.064461 310.1659 at 10iterations 5.149263 156.3160 at 20iterations 2.924047 77.90244 at 30iterations 1.649553 44.87261 at 40iterations 0.9293166 24.66235 at 50iterations 0.5226852 12.46436 at 60iterations 0.2932361 6.034348 at 70iterations 0.1641787 3.394788 at 80iterations 9.2137471E-02 1.949556 at 90iterations 5.1776439E-02 1.069221 at 100iterations 2.8937899E-02 0.6455612 at 110iterations 1.6205093E-02 0.3292389 at 120iterations 9.0741776E-03 0.1857610 at 130iterations 5.0775320E-03 0.1029148 at 140iterations 2.8398614E-03 5.9337616E-02 at 150iterations 1.5907309E-03 3.7609100E-02 at 160iterations 8.8844285E-04 1.8022537E-02 at 170iterations 4.9716450E-04 9.7742081E-03 at 180iterations finished qdiffx linear iterations at : 17:01:30 total time elapsed so far: 11.09000 # loops : 180 mean,max change (kT/e) : 4.9716450E-04 9.7742081E-03 energy calculations done at 11.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.28000 DelPhi exited at 17:01:32 11.284u 0.179s 0:12.92 88.6% 0+0k 0+0io 0pf+0w