Mon Oct 10 14:26:02 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 14:26:03 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2612 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6041579 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): -3.169000 55.75600 ymin,ymax (A): -11.63100 44.57400 zmin,zma (A): -11.31100 46.00100 x,y,z range (A): 58.92500 56.20500 57.31200 scale (grids/A): 0.6041579 object centre (A): 26.29350 16.47150 17.34500 number of atom coordinates read : 2612 total number of charged atoms : 2463 net assigned charge : -2.999994 assigned positive charge : 388.5009 centred at (gu) : 92.45863 91.47283 89.26830 assigned negative charge : -391.5015 centred at (gu) : 92.27235 91.45131 89.28307 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6257 nv = 96 ne = 84 npr = 52490 no. pairs analyzed = 52490 no. exposed pairs = 3552 no. arc points = 24652 no. surface atoms = 1193 nbur = 1419 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 292 mr = 3064 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3500000 number of dielectric boundary points 3463 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2486 ## 257 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7835 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2514275E-09 -1.9505701E-09 midg,1,midg; midg,igrid,midg -1.8591272E-09 -1.0765382E-09 1,midg,midg; igrid,midg,midg -5.5062799E-09 1.0501600E-08 gauss-seidel spectral radius is 0.9858230 estimated iterations to convergence 69 setup time was (sec) 0.5800000 now iterating at: 14:26:03 rms-change max change #iterations 0.1135685 19.42614 at 10iterations 9.5621962E-03 1.378739 at 20iterations 8.2233257E-04 0.1140785 at 30iterations 7.4326606E-05 1.1936188E-02 at 40iterations 6.8812378E-06 1.0957718E-03 at 50iterations finished qdiffx linear iterations at : 14:26:06 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 6.8812378E-06 1.0957718E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 14:26:08 3.417u 0.158s 0:05.56 64.0% 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 14:26:08 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2612 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: 1.812474 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): -3.169000 55.75600 ymin,ymax (A): -11.63100 44.57400 zmin,zma (A): -11.31100 46.00100 x,y,z range (A): 58.92500 56.20500 57.31200 scale (grids/A): 1.812474 object centre (A): 26.29350 16.47150 17.34500 number of atom coordinates read : 2612 total number of charged atoms : 2463 net assigned charge : -2.999994 assigned positive charge : 388.5009 centred at (gu) : 97.37517 94.41776 87.80441 assigned negative charge : -391.5015 centred at (gu) : 96.81685 94.35381 87.84891 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 67715 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24652 grid for indexing accessible points = 1.400000 m= 21549 mr = 44479 m= 2818 mr = 14501 m= 166 mr = 1471 m= 2 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 31745 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 184 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 19233 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) : 0.6041579 object centre at (A) : 26.29350 16.47150 17.34500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4552051E-02 -7.2567100E-03 midg,1,midg; midg,igrid,midg -2.5764322E-02 -3.4275159E-02 1,midg,midg; igrid,midg,midg -1.4943030E-02 6.3129373E-02 gauss-seidel spectral radius is 0.9984917 estimated iterations to convergence 204 setup time was (sec) 0.8700000 now iterating at: 14:26:09 rms-change max change #iterations 3.843998 201.3716 at 10iterations 1.723719 76.82979 at 20iterations 0.7757190 25.90048 at 30iterations 0.3463105 11.18925 at 40iterations 0.1563810 5.054378 at 50iterations 7.0298873E-02 2.384830 at 60iterations 3.1553119E-02 1.111562 at 70iterations 1.4219130E-02 0.4804993 at 80iterations 6.4056208E-03 0.2279716 at 90iterations 2.8750552E-03 0.1008472 at 100iterations 1.3016526E-03 4.7531128E-02 at 110iterations 5.8653549E-04 2.0694733E-02 at 120iterations finished qdiffx linear iterations at : 14:26:16 total time elapsed so far: 7.510000 # loops : 120 mean,max change (kT/e) : 5.8653549E-04 2.0694733E-02 energy calculations done at 7.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 14:26:17 7.732u 0.240s 0:08.49 93.8% 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 14:26:17 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 = 2612 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: 2.718710 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): -3.169000 55.75600 ymin,ymax (A): -11.63100 44.57400 zmin,zma (A): -11.31100 46.00100 x,y,z range (A): 58.92500 56.20500 57.31200 scale (grids/A): 2.718710 object centre (A): 26.29350 16.47150 17.34500 number of atom coordinates read : 2612 total number of charged atoms : 2463 net assigned charge : -2.999994 assigned positive charge : 388.5009 centred at (gu) : 101.0626 96.62660 86.70642 assigned negative charge : -391.5015 centred at (gu) : 100.2253 96.53060 86.77338 start vw surface at 0.1900000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 156934 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24652 grid for indexing accessible points = 1.400000 m= 72311 mr = 109075 m= 23012 mr = 56299 m= 4797 mr = 17064 m= 669 mr = 3156 m= 37 mr = 437 m= 0 mr = 11 time to grow re-entrant surface = 0.7400001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.350000 number of dielectric boundary points 71718 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 19699 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) : 1.812474 object centre at (A) : 26.29350 16.47150 17.34500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3164046 -9.3922809E-02 midg,1,midg; midg,igrid,midg -0.3321543 -0.3652523 1,midg,midg; igrid,midg,midg -3.4830920E-02 1.318577 gauss-seidel spectral radius is 0.9992291 estimated iterations to convergence 284 setup time was (sec) 1.680000 now iterating at: 14:26:19 rms-change max change #iterations 9.287203 272.1891 at 10iterations 5.384478 122.4699 at 20iterations 3.100178 74.78038 at 30iterations 1.775896 37.12856 at 40iterations 1.013906 21.35721 at 50iterations 0.5771606 13.25252 at 60iterations 0.3295806 6.534539 at 70iterations 0.1870080 4.107434 at 80iterations 0.1066194 2.094232 at 90iterations 6.0488142E-02 1.152689 at 100iterations 3.4392569E-02 0.6744766 at 110iterations 1.9503102E-02 0.3593044 at 120iterations 1.1070235E-02 0.2293415 at 130iterations 6.2973662E-03 0.1235256 at 140iterations 3.5646060E-03 6.5635443E-02 at 150iterations 2.0259223E-03 4.2638779E-02 at 160iterations 1.1526078E-03 2.3399353E-02 at 170iterations 6.5569358E-04 1.2746811E-02 at 180iterations finished qdiffx linear iterations at : 14:26:30 total time elapsed so far: 12.78000 # loops : 180 mean,max change (kT/e) : 6.5569358E-04 1.2746811E-02 energy calculations done at 12.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.98000 DelPhi exited at 14:26:31 12.982u 0.234s 0:13.72 96.2% 0+0k 0+0io 0pf+0w