Mon Oct 10 14:00:03 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 14:00:03 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: 234 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2018 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: 0.6038606 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): -24.48600 34.46800 ymin,ymax (A): -17.91600 20.00600 zmin,zma (A): -3.754000 38.29800 x,y,z range (A): 58.95400 37.92200 42.05200 scale (grids/A): 0.6038606 object centre (A): 4.991001 1.045000 17.27200 number of atom coordinates read : 2018 total number of charged atoms : 1866 net assigned charge : 2.000005 assigned positive charge : 294.6069 centred at (gu) : 90.07481 90.05739 90.29668 assigned negative charge : -292.6073 centred at (gu) : 90.10455 90.13402 90.43476 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 4944 nv = 96 ne = 84 npr = 40776 no. pairs analyzed = 40776 no. exposed pairs = 2554 no. arc points = 17558 no. surface atoms = 883 nbur = 1135 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 254 mr = 2678 m= 1 mr = 23 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 0.2500000 number of dielectric boundary points 2498 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1798 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 5989 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.8663176E-09 -3.5986043E-09 midg,1,midg; midg,igrid,midg 3.3039020E-09 -1.4238717E-09 1,midg,midg; igrid,midg,midg 1.8791442E-09 6.7623442E-11 gauss-seidel spectral radius is 0.9857566 estimated iterations to convergence 69 setup time was (sec) 0.5400000 now iterating at: 14:00:04 rms-change max change #iterations 9.9814199E-02 19.08852 at 10iterations 8.4766671E-03 1.497641 at 20iterations 7.1804092E-04 0.1183777 at 30iterations 6.3079780E-05 1.0387421E-02 at 40iterations 5.4087800E-06 8.3827972E-04 at 50iterations finished qdiffx linear iterations at : 14:00:08 total time elapsed so far: 4.440000 # loops : 50 mean,max change (kT/e) : 5.4087800E-06 8.3827972E-04 energy calculations done at 4.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.630000 DelPhi exited at 14:00:08 4.630u 0.355s 0:05.56 89.5% 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 Mon Oct 10 2011 at 14:00:08 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: 234 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2018 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: 1.811582 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): -24.48600 34.46800 ymin,ymax (A): -17.91600 20.00600 zmin,zma (A): -3.754000 38.29800 x,y,z range (A): 58.95400 37.92200 42.05200 scale (grids/A): 1.811582 object centre (A): 4.991001 1.045000 17.27200 number of atom coordinates read : 2018 total number of charged atoms : 1866 net assigned charge : 2.000005 assigned positive charge : 294.6069 centred at (gu) : 90.22458 90.17213 90.88991 assigned negative charge : -292.6073 centred at (gu) : 90.31387 90.40225 91.30453 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 52924 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17558 grid for indexing accessible points = 1.400000 m= 19394 mr = 36043 m= 2862 mr = 14547 m= 135 mr = 1801 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 22885 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 14572 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) : 0.6038606 object centre at (A) : 4.991001 1.045000 17.27200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9052116E-03 -8.4111821E-03 midg,1,midg; midg,igrid,midg 1.5678202E-03 -3.4796121E-03 1,midg,midg; igrid,midg,midg 4.2562250E-02 2.9865028E-02 gauss-seidel spectral radius is 0.9984244 estimated iterations to convergence 200 setup time was (sec) 0.7800000 now iterating at: 14:00:09 rms-change max change #iterations 3.275369 149.1242 at 10iterations 1.444543 56.91098 at 20iterations 0.6406103 25.69050 at 30iterations 0.2826694 11.65662 at 40iterations 0.1248608 5.106625 at 50iterations 5.5213630E-02 2.377137 at 60iterations 2.4522368E-02 0.8482504 at 70iterations 1.0817352E-02 0.4314346 at 80iterations 4.7983271E-03 0.1826706 at 90iterations 2.1153947E-03 8.3198547E-02 at 100iterations 9.3995564E-04 3.2060623E-02 at 110iterations 4.1621964E-04 1.6740799E-02 at 120iterations finished qdiffx linear iterations at : 14:00:19 total time elapsed so far: 9.950000 # loops : 120 mean,max change (kT/e) : 4.1621964E-04 1.6740799E-02 energy calculations done at 9.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.14000 DelPhi exited at 14:00:20 10.139u 0.324s 0:11.94 87.5% 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 Mon Oct 10 2011 at 14:00:20 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: 234 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2018 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: 2.717373 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): -24.48600 34.46800 ymin,ymax (A): -17.91600 20.00600 zmin,zma (A): -3.754000 38.29800 x,y,z range (A): 58.95400 37.92200 42.05200 scale (grids/A): 2.717373 object centre (A): 4.991001 1.045000 17.27200 number of atom coordinates read : 2018 total number of charged atoms : 1866 net assigned charge : 2.000005 assigned positive charge : 294.6069 centred at (gu) : 90.33681 90.25816 91.33488 assigned negative charge : -292.6073 centred at (gu) : 90.47090 90.60340 91.95685 start vw surface at 0.1200000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 122172 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17558 grid for indexing accessible points = 1.400000 m= 61945 mr = 87086 m= 22730 mr = 50945 m= 5155 mr = 18580 m= 602 mr = 3959 m= 31 mr = 407 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.110000 number of dielectric boundary points 51655 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 14922 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) : 1.811582 object centre at (A) : 4.991001 1.045000 17.27200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8958553E-02 -7.6690860E-02 midg,1,midg; midg,igrid,midg -1.1322983E-02 -3.1237725E-02 1,midg,midg; igrid,midg,midg 0.4701272 0.3527877 gauss-seidel spectral radius is 0.9991832 estimated iterations to convergence 276 setup time was (sec) 1.520000 now iterating at: 14:00:22 rms-change max change #iterations 7.991293 334.4583 at 10iterations 4.568134 134.6692 at 20iterations 2.578652 59.94290 at 30iterations 1.456177 33.15386 at 40iterations 0.8157034 20.15955 at 50iterations 0.4574970 11.44511 at 60iterations 0.2561094 5.356512 at 70iterations 0.1433180 2.934986 at 80iterations 8.0192000E-02 1.657148 at 90iterations 4.4927843E-02 1.024795 at 100iterations 2.5066379E-02 0.5408974 at 110iterations 1.4004092E-02 0.2947435 at 120iterations 7.8044035E-03 0.1710701 at 130iterations 4.3553398E-03 9.3910933E-02 at 140iterations 2.4338656E-03 5.0096512E-02 at 150iterations 1.3584425E-03 3.2112122E-02 at 160iterations 7.5772131E-04 1.6819000E-02 at 170iterations 4.2290735E-04 8.8043213E-03 at 180iterations finished qdiffx linear iterations at : 14:00:37 total time elapsed so far: 15.73000 # loops : 180 mean,max change (kT/e) : 4.2290735E-04 8.8043213E-03 energy calculations done at 15.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.91000 DelPhi exited at 14:00:37 15.915u 0.415s 0:17.04 95.7% 0+0k 0+0io 0pf+0w