Tue Oct 11 04:47:29 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 Tue Oct 11 2011 at 04:47:29 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 = 2713 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: 0.6421704 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): -11.45800 36.87200 ymin,ymax (A): -26.08100 22.56900 zmin,zma (A): -10.19400 45.24300 x,y,z range (A): 48.33000 48.65000 55.43700 scale (grids/A): 0.6421704 object centre (A): 12.70700 -1.756000 17.52450 number of atom coordinates read : 2713 total number of charged atoms : 2564 net assigned charge : 1.500015 assigned positive charge : 410.8337 centred at (gu) : 90.04760 90.57471 92.13580 assigned negative charge : -409.3343 centred at (gu) : 89.81270 90.42067 92.03748 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7299 nv = 96 ne = 84 npr = 55644 no. pairs analyzed = 55644 no. exposed pairs = 3349 no. arc points = 23355 no. surface atoms = 1132 nbur = 1581 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 412 mr = 4042 m= 0 mr = 37 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.3100000 number of dielectric boundary points 3632 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2343 ## 237 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8921 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.9044068E-09 2.3220311E-08 midg,1,midg; midg,igrid,midg -1.6251233E-08 2.4471364E-08 1,midg,midg; igrid,midg,midg -2.9080176E-08 3.1999676E-08 gauss-seidel spectral radius is 0.9874403 estimated iterations to convergence 73 setup time was (sec) 0.5200000 now iterating at: 04:47:30 rms-change max change #iterations 0.1530818 22.57125 at 10iterations 1.5484802E-02 1.983208 at 20iterations 1.6205070E-03 0.2277050 at 30iterations 1.7948028E-04 2.8453827E-02 at 40iterations 2.6750173E-05 4.4193268E-03 at 50iterations finished qdiffx linear iterations at : 04:47:32 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 2.6750173E-05 4.4193268E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 04:47:33 3.116u 0.137s 0:03.58 90.5% 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 Tue Oct 11 2011 at 04:47:33 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 = 2713 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: 1.926511 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): -11.45800 36.87200 ymin,ymax (A): -26.08100 22.56900 zmin,zma (A): -10.19400 45.24300 x,y,z range (A): 48.33000 48.65000 55.43700 scale (grids/A): 1.926511 object centre (A): 12.70700 -1.756000 17.52450 number of atom coordinates read : 2713 total number of charged atoms : 2564 net assigned charge : 1.500015 assigned positive charge : 410.8337 centred at (gu) : 90.14224 91.72380 96.40674 assigned negative charge : -409.3343 centred at (gu) : 89.43784 91.26145 96.11230 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 78726 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23355 grid for indexing accessible points = 1.400000 m= 28870 mr = 54923 m= 4346 mr = 21221 m= 243 mr = 2609 m= 3 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 188 time to turn everything in is 0.5500000 number of dielectric boundary points 33375 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 158 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 20178 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) : 0.6421704 object centre at (A) : 12.70700 -1.756000 17.52450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.7869312E-02 4.3740571E-03 midg,1,midg; midg,igrid,midg -1.5685735E-02 1.9040082E-02 1,midg,midg; igrid,midg,midg -1.0540186E-02 4.9579401E-02 gauss-seidel spectral radius is 0.9986734 estimated iterations to convergence 218 setup time was (sec) 0.8100000 now iterating at: 04:47:34 rms-change max change #iterations 4.475610 194.9684 at 10iterations 2.118988 75.27524 at 20iterations 1.004029 30.68293 at 30iterations 0.4768714 16.45030 at 40iterations 0.2261754 7.741791 at 50iterations 0.1074509 3.185383 at 60iterations 5.0776083E-02 1.475227 at 70iterations 2.4239732E-02 0.7149277 at 80iterations 1.1461631E-02 0.3761806 at 90iterations 5.4397862E-03 0.1540489 at 100iterations 2.5856234E-03 7.6761246E-02 at 110iterations 1.2246945E-03 3.7685394E-02 at 120iterations finished qdiffx linear iterations at : 04:47:40 total time elapsed so far: 6.820000 # loops : 120 mean,max change (kT/e) : 1.2246945E-03 3.7685394E-02 energy calculations done at 6.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.990000 DelPhi exited at 04:47:41 6.995u 0.176s 0:07.92 90.4% 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 Oct 11 2011 at 04:47:41 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 = 2713 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: 2.889767 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): -11.45800 36.87200 ymin,ymax (A): -26.08100 22.56900 zmin,zma (A): -10.19400 45.24300 x,y,z range (A): 48.33000 48.65000 55.43700 scale (grids/A): 2.889767 object centre (A): 12.70700 -1.756000 17.52450 number of atom coordinates read : 2713 total number of charged atoms : 2564 net assigned charge : 1.500015 assigned positive charge : 410.8337 centred at (gu) : 90.21322 92.58547 99.61001 assigned negative charge : -409.3343 centred at (gu) : 89.15681 91.89217 99.16836 start vw surface at 0.1600000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 182027 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23355 grid for indexing accessible points = 1.400000 m= 92952 mr = 132761 m= 33561 mr = 76094 m= 7818 mr = 27019 m= 991 mr = 5682 m= 58 mr = 580 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 646 time to turn everything in is 1.390000 number of dielectric boundary points 75256 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 20512 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) : 1.926511 object centre at (A) : 12.70700 -1.756000 17.52450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5409189 0.2322754 midg,1,midg; midg,igrid,midg -0.1903798 0.2021251 1,midg,midg; igrid,midg,midg -3.9102670E-02 0.4194744 gauss-seidel spectral radius is 0.9992678 estimated iterations to convergence 292 setup time was (sec) 1.660000 now iterating at: 04:47:43 rms-change max change #iterations 10.48147 400.2734 at 10iterations 6.151375 138.0615 at 20iterations 3.598842 83.48556 at 30iterations 2.102151 53.92781 at 40iterations 1.223564 27.74658 at 50iterations 0.7095715 13.34903 at 60iterations 0.4105580 7.722410 at 70iterations 0.2387407 4.151123 at 80iterations 0.1380777 2.591583 at 90iterations 8.0060199E-02 1.437826 at 100iterations 4.6302728E-02 0.9012666 at 110iterations 2.6835758E-02 0.4443007 at 120iterations 1.5486109E-02 0.2702026 at 130iterations 8.9864740E-03 0.1648407 at 140iterations 5.2118851E-03 0.1021805 at 150iterations 3.0401952E-03 5.6713104E-02 at 160iterations 1.7850931E-03 3.2482147E-02 at 170iterations 1.0607596E-03 1.9416809E-02 at 180iterations finished qdiffx linear iterations at : 04:47:52 total time elapsed so far: 11.07000 # loops : 180 mean,max change (kT/e) : 1.0607596E-03 1.9416809E-02 energy calculations done at 11.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.25000 DelPhi exited at 04:47:53 11.256u 0.174s 0:12.07 94.6% 0+0k 0+0io 0pf+0w