Tue Nov 22 14:13:31 PST 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 Tue Nov 22 2011 at 14:13:35 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 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: 0.6138566 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): -35.40300 9.708000 ymin,ymax (A): 0.8890001 41.82100 zmin,zma (A): -1.642000 56.35200 x,y,z range (A): 45.11100 40.93200 57.99400 scale (grids/A): 0.6138566 object centre (A): -12.84750 21.35500 27.35500 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 5.000007 assigned positive charge : 291.4739 centred at (gu) : 90.59642 89.49537 90.35022 assigned negative charge : -286.4742 centred at (gu) : 90.56822 89.55120 90.34875 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4943 nv = 96 ne = 84 npr = 40814 no. pairs analyzed = 40814 no. exposed pairs = 2485 no. arc points = 17174 no. surface atoms = 840 nbur = 1128 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 225 mr = 2703 m= 0 mr = 17 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 2448 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1719 ## 184 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 6003 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0141190E-09 3.6334202E-09 midg,1,midg; midg,igrid,midg 6.2390217E-09 9.1586927E-10 1,midg,midg; igrid,midg,midg 1.8994268E-09 5.0822808E-09 gauss-seidel spectral radius is 0.9862040 estimated iterations to convergence 70 setup time was (sec) 0.4400000 now iterating at: 14:13:39 rms-change max change #iterations 0.1065127 16.30559 at 10iterations 9.3423761E-03 1.502548 at 20iterations 8.3581137E-04 0.1572762 at 30iterations 7.4407217E-05 1.2654305E-02 at 40iterations 6.6750495E-06 1.1444092E-03 at 50iterations finished qdiffx linear iterations at : 14:13:47 total time elapsed so far: 3.020000 # loops : 50 mean,max change (kT/e) : 6.6750495E-06 1.1444092E-03 energy calculations done at 3.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.200000 DelPhi exited at 14:13:58 3.199u 0.183s 0:24.00 14.0% 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 Tue Nov 22 2011 at 14:14:03 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 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: 1.841570 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): -35.40300 9.708000 ymin,ymax (A): 0.8890001 41.82100 zmin,zma (A): -1.642000 56.35200 x,y,z range (A): 45.11100 40.93200 57.99400 scale (grids/A): 1.841570 object centre (A): -12.84750 21.35500 27.35500 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 5.000007 assigned positive charge : 291.4739 centred at (gu) : 91.78924 88.48593 91.05070 assigned negative charge : -286.4742 centred at (gu) : 91.70504 88.65391 91.04633 start vw surface at 0.1200000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 53346 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17174 grid for indexing accessible points = 1.400000 m= 19275 mr = 36521 m= 2708 mr = 14266 m= 148 mr = 1664 m= 1 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 22956 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 125 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 14389 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) : 0.6138566 object centre at (A) : -12.84750 21.35500 27.35500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8566929E-02 3.0537160E-02 midg,1,midg; midg,igrid,midg 4.9690320E-03 1.2894052E-03 1,midg,midg; igrid,midg,midg 3.3662294E-03 -2.2857271E-03 gauss-seidel spectral radius is 0.9984638 estimated iterations to convergence 202 setup time was (sec) 0.6200000 now iterating at: 14:14:10 rms-change max change #iterations 3.350547 178.1118 at 10iterations 1.501725 63.27993 at 20iterations 0.6699778 24.63017 at 30iterations 0.2999938 10.60295 at 40iterations 0.1334730 4.713373 at 50iterations 5.9767433E-02 2.251022 at 60iterations 2.6742158E-02 0.9229145 at 70iterations 1.1894458E-02 0.4524765 at 80iterations 5.3547937E-03 0.1997604 at 90iterations 2.3861583E-03 9.3304634E-02 at 100iterations 1.0640491E-03 3.9915085E-02 at 110iterations 4.7936616E-04 1.9562244E-02 at 120iterations finished qdiffx linear iterations at : 14:14:30 total time elapsed so far: 6.620000 # loops : 120 mean,max change (kT/e) : 4.7936616E-04 1.9562244E-02 energy calculations done at 6.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.790000 DelPhi exited at 14:14:34 6.794u 0.168s 0:30.97 22.4% 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 Nov 22 2011 at 14:14:38 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 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: 2.762355 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): -35.40300 9.708000 ymin,ymax (A): 0.8890001 41.82100 zmin,zma (A): -1.642000 56.35200 x,y,z range (A): 45.11100 40.93200 57.99400 scale (grids/A): 2.762355 object centre (A): -12.84750 21.35500 27.35500 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 5.000007 assigned positive charge : 291.4739 centred at (gu) : 92.68372 87.72881 91.57602 assigned negative charge : -286.4742 centred at (gu) : 92.55748 87.98090 91.56945 start vw surface at 0.1100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 123089 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17174 grid for indexing accessible points = 1.400000 m= 62375 mr = 88321 m= 22212 mr = 51110 m= 4851 mr = 17972 m= 625 mr = 3600 m= 42 mr = 436 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9300000 number of dielectric boundary points 51735 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 14685 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) : 1.841570 object centre at (A) : -12.84750 21.35500 27.35500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.1251392E-02 0.2558301 midg,1,midg; midg,igrid,midg 1.3663908E-02 6.7191278E-03 1,midg,midg; igrid,midg,midg 8.5063633E-03 -7.1012318E-02 gauss-seidel spectral radius is 0.9991937 estimated iterations to convergence 278 setup time was (sec) 1.210000 now iterating at: 14:14:45 rms-change max change #iterations 8.027968 296.3442 at 10iterations 4.596563 109.2341 at 20iterations 2.603758 61.86857 at 30iterations 1.464583 32.78489 at 40iterations 0.8244189 18.29814 at 50iterations 0.4641426 10.29012 at 60iterations 0.2597947 5.413597 at 70iterations 0.1455807 3.243469 at 80iterations 8.1654221E-02 1.741028 at 90iterations 4.5702629E-02 0.9786911 at 100iterations 2.5623977E-02 0.5543509 at 110iterations 1.4388054E-02 0.3023491 at 120iterations 8.0389762E-03 0.1752796 at 130iterations 4.4979593E-03 8.8918447E-02 at 140iterations 2.5131248E-03 5.6047440E-02 at 150iterations 1.4080514E-03 3.1017303E-02 at 160iterations 7.8867993E-04 1.6311646E-02 at 170iterations 4.4105889E-04 9.3045235E-03 at 180iterations finished qdiffx linear iterations at : 14:15:15 total time elapsed so far: 11.15000 # loops : 180 mean,max change (kT/e) : 4.4105889E-04 9.3045235E-03 energy calculations done at 11.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.33000 DelPhi exited at 14:15:18 11.329u 0.181s 0:40.35 28.5% 0+0k 0+0io 0pf+0w