Sun Oct 9 22:13:52 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 Sun Oct 9 2011 at 22:13:52 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2579 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: 0.6435286 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): -15.75500 39.56500 ymin,ymax (A): -16.79500 38.26500 zmin,zma (A): -3.813000 49.18700 x,y,z range (A): 55.32000 55.06000 53.00000 scale (grids/A): 0.6435286 object centre (A): 11.90500 10.73500 22.68700 number of atom coordinates read : 2579 total number of charged atoms : 2435 net assigned charge : 5.000013 assigned positive charge : 388.9828 centred at (gu) : 89.93916 88.87633 90.17321 assigned negative charge : -383.9836 centred at (gu) : 89.90418 88.80077 90.20623 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6983 nv = 96 ne = 84 npr = 52680 no. pairs analyzed = 52680 no. exposed pairs = 3089 no. arc points = 22182 no. surface atoms = 1046 nbur = 1533 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 397 mr = 3821 m= 2 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 87 time to turn everything in is 0.3300000 number of dielectric boundary points 3513 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2259 ## 246 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8563 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1913801E-08 4.1114809E-09 midg,1,midg; midg,igrid,midg -2.0359958E-09 1.3962580E-08 1,midg,midg; igrid,midg,midg 3.7692254E-09 1.2440871E-08 gauss-seidel spectral radius is 0.9874876 estimated iterations to convergence 73 setup time was (sec) 0.5600000 now iterating at: 22:13:53 rms-change max change #iterations 0.1478051 24.71782 at 10iterations 1.4927083E-02 2.537855 at 20iterations 1.4955481E-03 0.2112556 at 30iterations 1.4839222E-04 2.0745277E-02 at 40iterations 1.4937763E-05 2.2287369E-03 at 50iterations finished qdiffx linear iterations at : 22:13:56 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.4937763E-05 2.2287369E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 22:13:56 3.375u 0.125s 0:03.78 92.3% 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 Sun Oct 9 2011 at 22:13:56 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 = 2579 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: 1.930586 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): -15.75500 39.56500 ymin,ymax (A): -16.79500 38.26500 zmin,zma (A): -3.813000 49.18700 x,y,z range (A): 55.32000 55.06000 53.00000 scale (grids/A): 1.930586 object centre (A): 11.90500 10.73500 22.68700 number of atom coordinates read : 2579 total number of charged atoms : 2435 net assigned charge : 5.000013 assigned positive charge : 388.9828 centred at (gu) : 89.81700 86.62852 90.51924 assigned negative charge : -383.9836 centred at (gu) : 89.71230 86.40205 90.61844 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 75847 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22182 grid for indexing accessible points = 1.400000 m= 25690 mr = 52074 m= 3990 mr = 18672 m= 267 mr = 2466 m= 4 mr = 135 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1653 time to turn everything in is 0.5700000 number of dielectric boundary points 32451 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 150 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 19183 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) : 0.6435286 object centre at (A) : 11.90500 10.73500 22.68700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4737527E-02 -8.7194545E-03 midg,1,midg; midg,igrid,midg 1.6561398E-02 -1.1546503E-02 1,midg,midg; igrid,midg,midg 1.0786345E-02 2.0631594E-03 gauss-seidel spectral radius is 0.9986634 estimated iterations to convergence 217 setup time was (sec) 0.8500000 now iterating at: 22:13:57 rms-change max change #iterations 4.284618 190.8500 at 10iterations 2.024566 66.83209 at 20iterations 0.9574180 31.98316 at 30iterations 0.4505775 14.98434 at 40iterations 0.2122218 7.081966 at 50iterations 9.9858224E-02 3.366726 at 60iterations 4.7193024E-02 1.541077 at 70iterations 2.2239547E-02 0.7523313 at 80iterations 1.0498445E-02 0.3352451 at 90iterations 4.9566003E-03 0.1654358 at 100iterations 2.3337547E-03 7.8616142E-02 at 110iterations 1.1019098E-03 3.6739349E-02 at 120iterations finished qdiffx linear iterations at : 22:14:04 total time elapsed so far: 7.360000 # loops : 120 mean,max change (kT/e) : 1.1019098E-03 3.6739349E-02 energy calculations done at 7.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.540000 DelPhi exited at 22:14:04 7.545u 0.173s 0:08.09 95.3% 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 Sun Oct 9 2011 at 22:14:04 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 = 2579 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: 2.895879 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): -15.75500 39.56500 ymin,ymax (A): -16.79500 38.26500 zmin,zma (A): -3.813000 49.18700 x,y,z range (A): 55.32000 55.06000 53.00000 scale (grids/A): 2.895879 object centre (A): 11.90500 10.73500 22.68700 number of atom coordinates read : 2579 total number of charged atoms : 2435 net assigned charge : 5.000013 assigned positive charge : 388.9828 centred at (gu) : 89.72555 84.94281 90.77859 assigned negative charge : -383.9836 centred at (gu) : 89.56840 84.60294 90.92764 start vw surface at 0.1500000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 175665 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22182 grid for indexing accessible points = 1.400000 m= 84631 mr = 126446 m= 29102 mr = 68841 m= 7119 mr = 23061 m= 1092 mr = 5409 m= 74 mr = 833 m= 0 mr = 37 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 5815 time to turn everything in is 1.420000 number of dielectric boundary points 73056 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 19478 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) : 1.930586 object centre at (A) : 11.90500 10.73500 22.68700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4769965 -0.2617511 midg,1,midg; midg,igrid,midg 0.2140260 -0.1933407 1,midg,midg; igrid,midg,midg -7.2225019E-02 0.1164659 gauss-seidel spectral radius is 0.9992682 estimated iterations to convergence 292 setup time was (sec) 1.730000 now iterating at: 22:14:06 rms-change max change #iterations 9.973522 339.2198 at 10iterations 5.798096 133.3286 at 20iterations 3.353486 62.98299 at 30iterations 1.935466 39.12587 at 40iterations 1.116340 20.44330 at 50iterations 0.6428553 11.39034 at 60iterations 0.3706179 6.292433 at 70iterations 0.2134968 4.169217 at 80iterations 0.1228774 2.226467 at 90iterations 7.0767306E-02 1.331689 at 100iterations 4.0729646E-02 0.7225270 at 110iterations 2.3399610E-02 0.3902245 at 120iterations 1.3486890E-02 0.2702506 at 130iterations 7.7575366E-03 0.1357284 at 140iterations 4.4653062E-03 8.5152388E-02 at 150iterations 2.5703481E-03 4.8390388E-02 at 160iterations 1.4787090E-03 2.4973869E-02 at 170iterations 8.5248583E-04 1.6036987E-02 at 180iterations finished qdiffx linear iterations at : 22:14:16 total time elapsed so far: 12.04000 # loops : 180 mean,max change (kT/e) : 8.5248583E-04 1.6036987E-02 energy calculations done at 12.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.23000 DelPhi exited at 22:14:17 12.233u 0.223s 0:12.73 97.8% 0+0k 0+0io 0pf+0w