Mon Oct 10 14:28:37 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 Mon Oct 10 2011 at 14:28:37 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2728 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: 0.6375815 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): 10.68700 66.52300 ymin,ymax (A): -32.53000 22.05600 zmin,zma (A): -101.7380 -48.19500 x,y,z range (A): 55.83600 54.58600 53.54300 scale (grids/A): 0.6375815 object centre (A): 38.60500 -5.237000 -74.96650 number of atom coordinates read : 2728 total number of charged atoms : 2600 net assigned charge : 4.000015 assigned positive charge : 403.2136 centred at (gu) : 90.49742 88.08700 90.41448 assigned negative charge : -399.2144 centred at (gu) : 90.39657 88.01120 90.54729 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7741 nv = 96 ne = 84 npr = 53280 no. pairs analyzed = 53280 no. exposed pairs = 3686 no. arc points = 26025 no. surface atoms = 1237 nbur = 1491 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 405 mr = 4069 m= 3 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.3600000 number of dielectric boundary points 4042 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2467 ## 240 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9076 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8521504E-08 -1.0379319E-08 midg,1,midg; midg,igrid,midg -4.6656186E-09 9.3472812E-09 1,midg,midg; igrid,midg,midg -5.1587135E-09 1.8666833E-08 gauss-seidel spectral radius is 0.9872792 estimated iterations to convergence 72 setup time was (sec) 0.6200000 now iterating at: 14:28:38 rms-change max change #iterations 0.1479378 21.70370 at 10iterations 1.4582038E-02 1.971626 at 20iterations 1.4188199E-03 0.1802826 at 30iterations 1.4030231E-04 2.0126343E-02 at 40iterations 1.3593713E-05 1.8417835E-03 at 50iterations finished qdiffx linear iterations at : 14:28:41 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 1.3593713E-05 1.8417835E-03 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.060000 DelPhi exited at 14:28:42 4.066u 0.277s 0:04.81 90.0% 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 14:28:42 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2728 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: 1.912744 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): 10.68700 66.52300 ymin,ymax (A): -32.53000 22.05600 zmin,zma (A): -101.7380 -48.19500 x,y,z range (A): 55.83600 54.58600 53.54300 scale (grids/A): 1.912744 object centre (A): 38.60500 -5.237000 -74.96650 number of atom coordinates read : 2728 total number of charged atoms : 2600 net assigned charge : 4.000015 assigned positive charge : 403.2136 centred at (gu) : 91.49168 84.26051 91.24252 assigned negative charge : -399.2144 centred at (gu) : 91.18931 84.03326 91.64156 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 82933 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26025 grid for indexing accessible points = 1.400000 m= 29310 mr = 56020 m= 4300 mr = 20977 m= 226 mr = 2633 m= 5 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 1213 time to turn everything in is 0.7200000 number of dielectric boundary points 37071 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 183 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 20460 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) : 0.6375815 object centre at (A) : 38.60500 -5.237000 -74.96650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3688323E-02 -2.5882574E-02 midg,1,midg; midg,igrid,midg -7.0849638E-03 1.5393714E-02 1,midg,midg; igrid,midg,midg -1.3498657E-02 4.2635132E-02 gauss-seidel spectral radius is 0.9986719 estimated iterations to convergence 217 setup time was (sec) 1.020000 now iterating at: 14:28:43 rms-change max change #iterations 4.366487 191.4542 at 10iterations 2.058753 76.74166 at 20iterations 0.9706622 31.75658 at 30iterations 0.4587733 16.63562 at 40iterations 0.2167196 6.299415 at 50iterations 0.1024674 3.659481 at 60iterations 4.8443019E-02 1.612911 at 70iterations 2.2892863E-02 0.6859417 at 80iterations 1.0812063E-02 0.3365583 at 90iterations 5.1074554E-03 0.1587915 at 100iterations 2.4188533E-03 7.4880600E-02 at 110iterations 1.1438533E-03 3.7883759E-02 at 120iterations finished qdiffx linear iterations at : 14:28:52 total time elapsed so far: 9.380000 # loops : 120 mean,max change (kT/e) : 1.1438533E-03 3.7883759E-02 energy calculations done at 9.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.550000 DelPhi exited at 14:28:52 9.557u 0.308s 0:10.26 96.0% 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 14:28:52 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2728 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: 2.869117 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): 10.68700 66.52300 ymin,ymax (A): -32.53000 22.05600 zmin,zma (A): -101.7380 -48.19500 x,y,z range (A): 55.83600 54.58600 53.54300 scale (grids/A): 2.869117 object centre (A): 38.60500 -5.237000 -74.96650 number of atom coordinates read : 2728 total number of charged atoms : 2600 net assigned charge : 4.000015 assigned positive charge : 403.2136 centred at (gu) : 92.23734 81.39071 91.86383 assigned negative charge : -399.2144 centred at (gu) : 91.78383 81.04991 92.46231 start vw surface at 0.1600000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 191831 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26025 grid for indexing accessible points = 1.400000 m= 95110 mr = 136289 m= 33467 mr = 76338 m= 7595 mr = 26394 m= 942 mr = 5634 m= 52 mr = 579 m= 0 mr = 25 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 4462 time to turn everything in is 1.890000 number of dielectric boundary points 83738 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.040000 number of grid points assigned charge 20793 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) : 1.912744 object centre at (A) : 38.60500 -5.237000 -74.96650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7179704 -0.2651233 midg,1,midg; midg,igrid,midg 9.3816660E-02 0.1432109 1,midg,midg; igrid,midg,midg -8.5378952E-02 0.5788122 gauss-seidel spectral radius is 0.9992813 estimated iterations to convergence 294 setup time was (sec) 2.210000 now iterating at: 14:28:55 rms-change max change #iterations 10.27622 339.8600 at 10iterations 6.057304 118.9796 at 20iterations 3.547047 74.93950 at 30iterations 2.074057 40.93003 at 40iterations 1.209412 24.60636 at 50iterations 0.7022985 13.64048 at 60iterations 0.4077540 7.446170 at 70iterations 0.2366962 4.138920 at 80iterations 0.1373285 2.555768 at 90iterations 7.9604127E-02 1.435123 at 100iterations 4.6155423E-02 0.8196602 at 110iterations 2.6733732E-02 0.5017338 at 120iterations 1.5503055E-02 0.2780609 at 130iterations 8.9665344E-03 0.1662350 at 140iterations 5.2043470E-03 9.4144821E-02 at 150iterations 3.0160851E-03 5.4689407E-02 at 160iterations 1.7444832E-03 3.1769753E-02 at 170iterations 1.0120359E-03 1.8123627E-02 at 180iterations finished qdiffx linear iterations at : 14:29:09 total time elapsed so far: 16.10000 # loops : 180 mean,max change (kT/e) : 1.0120359E-03 1.8123627E-02 energy calculations done at 16.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.28000 DelPhi exited at 14:29:09 16.284u 0.305s 0:16.99 97.5% 0+0k 0+0io 0pf+0w