Tue Oct 11 06:00:24 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+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 Oct 11 2011 at 06:00:24 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2028 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.7313516 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): 16.30000 63.05000 ymin,ymax (A): -3.704000 33.54000 zmin,zma (A): 23.30400 71.98100 x,y,z range (A): 46.75000 37.24400 48.67700 scale (grids/A): 0.7313516 object centre (A): 39.67500 14.91800 47.64250 number of atom coordinates read : 2028 total number of charged atoms : 1892 net assigned charge : 6.312006 assigned positive charge : 307.4101 centred at (gu) : 91.08751 89.62861 88.40533 assigned negative charge : -301.0981 centred at (gu) : 91.24666 89.68223 88.34324 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7429 nv = 96 ne = 84 npr = 40736 no. pairs analyzed = 40736 no. exposed pairs = 2458 no. arc points = 16973 no. surface atoms = 833 nbur = 1195 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 529 mr = 4311 m= 6 mr = 119 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 0.2700000 number of dielectric boundary points 3534 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1519 ## 142 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7964 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.8256820E-08 1.0674336E-07 midg,1,midg; midg,igrid,midg 1.4638096E-07 4.8037464E-08 1,midg,midg; igrid,midg,midg 1.7849598E-07 -4.4255451E-08 gauss-seidel spectral radius is 0.9902439 estimated iterations to convergence 82 setup time was (sec) 0.5200000 now iterating at: 06:00:25 rms-change max change #iterations 0.2279105 28.95881 at 10iterations 3.0089170E-02 3.541211 at 20iterations 4.1757785E-03 0.6949272 at 30iterations 6.8063126E-04 8.4140778E-02 at 40iterations 1.5572063E-04 2.0675659E-02 at 50iterations finished qdiffx linear iterations at : 06:00:28 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 1.5572063E-04 2.0675659E-02 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 06:00:28 3.323u 0.157s 0:04.02 86.3% 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 Oct 11 2011 at 06:00:28 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2028 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.194055 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): 16.30000 63.05000 ymin,ymax (A): -3.704000 33.54000 zmin,zma (A): 23.30400 71.98100 x,y,z range (A): 46.75000 37.24400 48.67700 scale (grids/A): 2.194055 object centre (A): 39.67500 14.91800 47.64250 number of atom coordinates read : 2028 total number of charged atoms : 1892 net assigned charge : 6.312006 assigned positive charge : 307.4101 centred at (gu) : 93.26260 88.88602 85.21599 assigned negative charge : -301.0981 centred at (gu) : 93.74016 89.04674 85.02982 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 78683 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16973 grid for indexing accessible points = 1.400000 m= 32877 mr = 56079 m= 7131 mr = 25403 m= 719 mr = 4940 m= 28 mr = 432 m= 0 mr = 2 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 32582 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 56 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 15068 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) : 0.7313516 object centre at (A) : 39.67500 14.91800 47.64250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0923325E-02 4.6075240E-02 midg,1,midg; midg,igrid,midg 3.3025596E-02 1.5300369E-02 1,midg,midg; igrid,midg,midg 4.2810481E-02 3.8407397E-02 gauss-seidel spectral radius is 0.9988911 estimated iterations to convergence 238 setup time was (sec) 0.8600000 now iterating at: 06:00:29 rms-change max change #iterations 4.823972 171.6767 at 10iterations 2.428186 79.77892 at 20iterations 1.233737 36.38886 at 30iterations 0.6268084 20.27550 at 40iterations 0.3157663 9.729244 at 50iterations 0.1600611 4.527555 at 60iterations 8.0954924E-02 2.488163 at 70iterations 4.1082945E-02 1.301861 at 80iterations 2.0807834E-02 0.6046448 at 90iterations 1.0615169E-02 0.3059692 at 100iterations 5.4038125E-03 0.1661682 at 110iterations 2.7838012E-03 9.0473652E-02 at 120iterations finished qdiffx linear iterations at : 06:00:36 total time elapsed so far: 7.360000 # loops : 120 mean,max change (kT/e) : 2.7838012E-03 9.0473652E-02 energy calculations done at 7.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.530000 DelPhi exited at 06:00:37 7.534u 0.232s 0:08.34 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 Tue Oct 11 2011 at 06:00:37 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2028 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 3.291082 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): 16.30000 63.05000 ymin,ymax (A): -3.704000 33.54000 zmin,zma (A): 23.30400 71.98100 x,y,z range (A): 46.75000 37.24400 48.67700 scale (grids/A): 3.291082 object centre (A): 39.67500 14.91800 47.64250 number of atom coordinates read : 2028 total number of charged atoms : 1892 net assigned charge : 6.312006 assigned positive charge : 307.4101 centred at (gu) : 94.89384 88.32899 82.82393 assigned negative charge : -301.0981 centred at (gu) : 95.61013 88.57016 82.54471 start vw surface at 0.1500000 fill in re-entrant regions at 0.8400000 boundary points on vw surface= 181305 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16973 grid for indexing accessible points = 1.400000 m= 101245 mr = 134974 m= 43191 mr = 84912 m= 13561 mr = 36150 m= 2989 mr = 10757 m= 465 mr = 2299 m= 25 mr = 361 m= 0 mr = 4 time to grow re-entrant surface = 0.9300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.880000 number of dielectric boundary points 73324 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.030000 number of grid points assigned charge 15136 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) : 2.194055 object centre at (A) : 39.67500 14.91800 47.64250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8437405E-02 0.2505765 midg,1,midg; midg,igrid,midg 0.2368065 0.1131913 1,midg,midg; igrid,midg,midg 0.3523177 0.7152668 gauss-seidel spectral radius is 0.9993132 estimated iterations to convergence 301 setup time was (sec) 2.210000 now iterating at: 06:00:39 rms-change max change #iterations 10.51538 417.5342 at 10iterations 6.261180 137.0403 at 20iterations 3.703703 77.19080 at 30iterations 2.203228 43.00936 at 40iterations 1.301126 22.07873 at 50iterations 0.7680664 15.47164 at 60iterations 0.4537713 7.649719 at 70iterations 0.2676672 4.756634 at 80iterations 0.1580142 3.176803 at 90iterations 9.3074173E-02 1.673969 at 100iterations 5.4877926E-02 0.8877664 at 110iterations 3.2423351E-02 0.5997715 at 120iterations 1.9233581E-02 0.3430958 at 130iterations 1.1537352E-02 0.1822739 at 140iterations 7.0335022E-03 0.1220474 at 150iterations 4.4205682E-03 7.5054169E-02 at 160iterations 2.8925762E-03 5.1239014E-02 at 170iterations 2.0171483E-03 3.4763336E-02 at 180iterations finished qdiffx linear iterations at : 06:00:52 total time elapsed so far: 14.68000 # loops : 180 mean,max change (kT/e) : 2.0171483E-03 3.4763336E-02 energy calculations done at 14.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.86000 DelPhi exited at 06:00:53 14.864u 0.249s 0:16.39 92.1% 0+0k 0+0io 0pf+0w