Mon Oct 10 16:58:12 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 16:58:12 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2913 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5302116 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): -34.26100 22.33800 ymin,ymax (A): -45.97500 8.203000 zmin,zma (A): -3.821000 63.32200 x,y,z range (A): 56.59900 54.17800 67.14300 scale (grids/A): 0.5302116 object centre (A): -5.961500 -18.88600 29.75050 number of atom coordinates read : 2913 total number of charged atoms : 2777 net assigned charge : 12.00002 assigned positive charge : 425.4802 centred at (gu) : 89.37585 89.52658 88.65123 assigned negative charge : -413.4810 centred at (gu) : 89.46555 89.59193 88.70830 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5419 nv = 96 ne = 84 npr = 56965 no. pairs analyzed = 56965 no. exposed pairs = 4131 no. arc points = 29436 no. surface atoms = 1381 nbur = 1532 mkacc time = 0.1000000 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 = 1.624000 m= 212 mr = 2445 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3178 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3000 ## 437 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 7162 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.1464607E-10 1.4289857E-10 midg,1,midg; midg,igrid,midg 6.8353972E-10 1.5018416E-10 1,midg,midg; igrid,midg,midg 8.0440010E-10 7.3977401E-11 gauss-seidel spectral radius is 0.9816809 estimated iterations to convergence 61 setup time was (sec) 0.4100000 now iterating at: 16:58:13 rms-change max change #iterations 6.0112942E-02 9.791790 at 10iterations 3.6443693E-03 0.6657104 at 20iterations 2.3203639E-04 3.9749146E-02 at 30iterations 1.5214331E-05 2.6111603E-03 at 40iterations 1.3034755E-06 2.1743774E-04 at 50iterations finished qdiffx linear iterations at : 16:58:16 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 1.3034755E-06 2.1743774E-04 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 16:58:16 3.481u 0.167s 0:04.00 91.0% 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 Mon Oct 10 2011 at 16:58:16 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 = 2913 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.590635 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): -34.26100 22.33800 ymin,ymax (A): -45.97500 8.203000 zmin,zma (A): -3.821000 63.32200 x,y,z range (A): 56.59900 54.17800 67.14300 scale (grids/A): 1.590635 object centre (A): -5.961500 -18.88600 29.75050 number of atom coordinates read : 2913 total number of charged atoms : 2777 net assigned charge : 12.00002 assigned positive charge : 425.4802 centred at (gu) : 88.12711 88.57898 85.95295 assigned negative charge : -413.4810 centred at (gu) : 88.39624 88.77505 86.12444 start vw surface at 0.1100000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 60047 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29436 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 16482 mr = 37845 m= 1440 mr = 10174 m= 32 mr = 524 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 613 time to turn everything in is 0.3100000 number of dielectric boundary points 29458 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 420 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 21140 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) : 0.5302116 object centre at (A) : -5.961500 -18.88600 29.75050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3900446E-02 -1.7580047E-02 midg,1,midg; midg,igrid,midg 1.2498250E-02 1.6728549E-03 1,midg,midg; igrid,midg,midg 2.0364385E-02 3.5451706E-03 gauss-seidel spectral radius is 0.9980876 estimated iterations to convergence 182 setup time was (sec) 0.5200000 now iterating at: 16:58:17 rms-change max change #iterations 2.989323 157.9759 at 10iterations 1.212124 49.25357 at 20iterations 0.4902622 19.09023 at 30iterations 0.1985192 7.893723 at 40iterations 8.0887750E-02 3.134392 at 50iterations 3.2773759E-02 1.198921 at 60iterations 1.3332404E-02 0.5474598 at 70iterations 5.4079103E-03 0.2025683 at 80iterations 2.2017269E-03 0.1014738 at 90iterations 8.9682516E-04 3.1735420E-02 at 100iterations 3.6424975E-04 1.4420986E-02 at 110iterations 1.4874293E-04 5.7659149E-03 at 120iterations finished qdiffx linear iterations at : 16:58:24 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 1.4874293E-04 5.7659149E-03 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 16:58:25 7.756u 0.241s 0:08.59 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 Mon Oct 10 2011 at 16:58:25 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 = 2913 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: 2.385952 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): -34.26100 22.33800 ymin,ymax (A): -45.97500 8.203000 zmin,zma (A): -3.821000 63.32200 x,y,z range (A): 56.59900 54.17800 67.14300 scale (grids/A): 2.385952 object centre (A): -5.961500 -18.88600 29.75050 number of atom coordinates read : 2913 total number of charged atoms : 2777 net assigned charge : 12.00002 assigned positive charge : 425.4802 centred at (gu) : 87.19056 87.86831 83.92937 assigned negative charge : -413.4810 centred at (gu) : 87.59420 88.16258 84.18661 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 139662 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29436 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 58448 mr = 93801 m= 14430 mr = 43409 m= 1868 mr = 9852 m= 85 mr = 976 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 1776 time to turn everything in is 0.7200000 number of dielectric boundary points 66438 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 22187 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) : 1.590635 object centre at (A) : -5.961500 -18.88600 29.75050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2362857 -0.3771820 midg,1,midg; midg,igrid,midg 0.1758374 2.7508700E-02 1,midg,midg; igrid,midg,midg 0.3691280 3.9250836E-02 gauss-seidel spectral radius is 0.9991097 estimated iterations to convergence 265 setup time was (sec) 0.9500000 now iterating at: 16:58:26 rms-change max change #iterations 8.042077 300.4252 at 10iterations 4.581971 141.9179 at 20iterations 2.568527 73.62067 at 30iterations 1.424316 41.73016 at 40iterations 0.7889209 22.11184 at 50iterations 0.4353663 10.58379 at 60iterations 0.2388290 5.387445 at 70iterations 0.1307958 2.888146 at 80iterations 7.1688570E-02 1.721207 at 90iterations 3.9163727E-02 0.9354362 at 100iterations 2.1341614E-02 0.4667692 at 110iterations 1.1654444E-02 0.2428770 at 120iterations 6.3484632E-03 0.1334162 at 130iterations 3.4574773E-03 7.7935576E-02 at 140iterations 1.8805797E-03 4.0122986E-02 at 150iterations 1.0283681E-03 2.3740768E-02 at 160iterations 5.5952911E-04 1.2161732E-02 at 170iterations 3.0504001E-04 6.5135956E-03 at 180iterations finished qdiffx linear iterations at : 16:58:37 total time elapsed so far: 12.15000 # loops : 180 mean,max change (kT/e) : 3.0504001E-04 6.5135956E-03 energy calculations done at 12.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.28000 DelPhi exited at 16:58:38 12.287u 0.209s 0:13.13 95.0% 0+0k 0+0io 0pf+0w