Sat Oct 15 13:15:03 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+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 Sat Oct 15 2011 at 13:15:03 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5496 !!! WARNING: HIR 147 has a net charge of 0.5140 !!! WARNING: GLM 509 has a net charge of -0.0940 !!! WARNING: HIR 516 has a net charge of 0.5140 !!! WARNING: HIZ 618 has a net charge of 0.2000 !!! WARNING: ZN3 3991 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.4862458 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): 7.796999 61.74600 ymin,ymax (A): 53.30000 126.5140 zmin,zma (A): 29.05700 96.74600 x,y,z range (A): 53.94900 73.21400 67.68900 scale (grids/A): 0.4862458 object centre (A): 34.77150 89.90700 62.90150 number of atom coordinates read : 5496 total number of charged atoms : 5327 net assigned charge : 5.034035 assigned positive charge : 859.5436 centred at (gu) : 89.52061 90.28780 90.57019 assigned negative charge : -854.5169 centred at (gu) : 89.53846 90.25542 90.43607 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7674 nv = 96 ne = 84 npr = 112016 no. pairs analyzed = 112016 no. exposed pairs = 6544 no. arc points = 45038 no. surface atoms = 2197 nbur = 3299 mkacc time = 0.2900000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.764000 m= 231 mr = 3981 m= 0 mr = 4 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.5700000 number of dielectric boundary points 3920 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4269 ## 733 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 10696 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0256026E-10 1.8622505E-10 midg,1,midg; midg,igrid,midg -1.1024739E-11 5.9945431E-11 1,midg,midg; igrid,midg,midg 4.6022713E-11 2.9192709E-12 gauss-seidel spectral radius is 0.9784158 estimated iterations to convergence 56 setup time was (sec) 0.9200000 now iterating at: 13:15:04 rms-change max change #iterations 5.7273272E-02 10.39045 at 10iterations 3.7718760E-03 0.5460529 at 20iterations 7.4300694E-04 0.1095886 at 30iterations 2.2996082E-04 3.2742262E-02 at 40iterations 7.5245072E-05 1.2408972E-02 at 50iterations finished qdiffx linear iterations at : 13:15:09 total time elapsed so far: 5.550000 # loops : 50 mean,max change (kT/e) : 7.5245072E-05 1.2408972E-02 energy calculations done at 5.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.730000 DelPhi exited at 13:15:10 5.731u 0.428s 0:06.61 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 Sat Oct 15 2011 at 13:15:10 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5496 !!! WARNING: HIR 147 has a net charge of 0.5140 !!! WARNING: GLM 509 has a net charge of -0.0940 !!! WARNING: HIR 516 has a net charge of 0.5140 !!! WARNING: HIZ 618 has a net charge of 0.2000 !!! WARNING: ZN3 3991 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.458737 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): 7.796999 61.74600 ymin,ymax (A): 53.30000 126.5140 zmin,zma (A): 29.05700 96.74600 x,y,z range (A): 53.94900 73.21400 67.68900 scale (grids/A): 1.458737 object centre (A): 34.77150 89.90700 62.90150 number of atom coordinates read : 5496 total number of charged atoms : 5327 net assigned charge : 5.034035 assigned positive charge : 859.5436 centred at (gu) : 88.55997 90.86189 91.70911 assigned negative charge : -854.5169 centred at (gu) : 88.61517 90.76605 91.30818 start vw surface at 0.1900000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 88850 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45038 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 23702 mr = 61521 m= 1627 mr = 15437 m= 24 mr = 612 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 1684 time to turn everything in is 0.7700000 number of dielectric boundary points 36633 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 691 ## 11 charges are in solution ## iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 39257 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) : 0.4862458 object centre at (A) : 34.77150 89.90700 62.90150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0922103E-02 1.3327322E-02 midg,1,midg; midg,igrid,midg -3.7637621E-03 5.0937664E-04 1,midg,midg; igrid,midg,midg 3.7347863E-03 1.8272920E-03 gauss-seidel spectral radius is 0.9979360 estimated iterations to convergence 175 setup time was (sec) 1.200000 now iterating at: 13:15:11 rms-change max change #iterations 3.732921 150.3550 at 10iterations 1.464107 50.86681 at 20iterations 0.5759704 19.39899 at 30iterations 0.2276091 7.570191 at 40iterations 8.9901745E-02 2.968506 at 50iterations 3.5521973E-02 1.088140 at 60iterations 1.4091065E-02 0.4696350 at 70iterations 5.6515364E-03 0.1987076 at 80iterations 2.3285511E-03 8.0333710E-02 at 90iterations 1.0193498E-03 3.3975601E-02 at 100iterations 4.9452245E-04 1.7078400E-02 at 110iterations 2.7418678E-04 8.6426735E-03 at 120iterations finished qdiffx linear iterations at : 13:15:23 total time elapsed so far: 12.85000 # loops : 120 mean,max change (kT/e) : 2.7418678E-04 8.6426735E-03 energy calculations done at 12.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.03000 DelPhi exited at 13:15:23 13.030u 0.531s 0:13.86 97.8% 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 Sat Oct 15 2011 at 13:15:24 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5496 !!! WARNING: HIR 147 has a net charge of 0.5140 !!! WARNING: GLM 509 has a net charge of -0.0940 !!! WARNING: HIR 516 has a net charge of 0.5140 !!! WARNING: HIZ 618 has a net charge of 0.2000 !!! WARNING: ZN3 3991 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.188106 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): 7.796999 61.74600 ymin,ymax (A): 53.30000 126.5140 zmin,zma (A): 29.05700 96.74600 x,y,z range (A): 53.94900 73.21400 67.68900 scale (grids/A): 2.188106 object centre (A): 34.77150 89.90700 62.90150 number of atom coordinates read : 5496 total number of charged atoms : 5327 net assigned charge : 5.034035 assigned positive charge : 859.5436 centred at (gu) : 87.83971 91.29241 92.56332 assigned negative charge : -854.5169 centred at (gu) : 87.92276 91.14872 91.96219 start vw surface at 0.1900000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 207765 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45038 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 87521 mr = 151655 m= 19512 mr = 67796 m= 2130 mr = 13743 m= 69 mr = 1170 m= 0 mr = 12 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 5568 time to turn everything in is 1.840000 number of dielectric boundary points 82621 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 117 iepsmp to db, and charging done at 2.010000 number of grid points assigned charge 42397 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) : 1.458737 object centre at (A) : 34.77150 89.90700 62.90150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1820659 0.2206043 midg,1,midg; midg,igrid,midg -0.1241489 -1.0207676E-02 1,midg,midg; igrid,midg,midg 7.4915469E-02 4.2729300E-02 gauss-seidel spectral radius is 0.9991140 estimated iterations to convergence 265 setup time was (sec) 2.260000 now iterating at: 13:15:26 rms-change max change #iterations 10.38412 264.9546 at 10iterations 5.819617 131.4795 at 20iterations 3.239501 68.44395 at 30iterations 1.794997 39.45809 at 40iterations 0.9891429 21.01719 at 50iterations 0.5452900 10.65866 at 60iterations 0.3002677 6.637674 at 70iterations 0.1645808 2.893144 at 80iterations 9.0339102E-02 1.614800 at 90iterations 4.9350459E-02 0.9185057 at 100iterations 2.7017927E-02 0.5565839 at 110iterations 1.4781577E-02 0.2813859 at 120iterations 8.0877496E-03 0.1614304 at 130iterations 4.4284184E-03 8.2859039E-02 at 140iterations 2.4151707E-03 4.3952942E-02 at 150iterations 1.3229678E-03 2.4892807E-02 at 160iterations 7.2457525E-04 1.3519287E-02 at 170iterations 3.9722727E-04 7.5225830E-03 at 180iterations finished qdiffx linear iterations at : 13:15:47 total time elapsed so far: 22.50000 # loops : 180 mean,max change (kT/e) : 3.9722727E-04 7.5225830E-03 energy calculations done at 22.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.66000 DelPhi exited at 13:15:47 22.665u 0.560s 0:23.69 98.0% 0+0k 0+0io 0pf+0w