Mon Oct 10 13:59:55 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 13:59:55 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1343 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7462217 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): -21.62700 21.08400 ymin,ymax (A): -61.17300 -13.46600 zmin,zma (A): 7.414000 45.50500 x,y,z range (A): 42.71100 47.70700 38.09100 scale (grids/A): 0.7462217 object centre (A): -0.2715006 -37.31950 26.45950 number of atom coordinates read : 1343 total number of charged atoms : 1273 net assigned charge : -0.4999965 assigned positive charge : 204.5722 centred at (gu) : 90.85918 91.13467 89.75060 assigned negative charge : -205.0722 centred at (gu) : 90.67924 91.01546 89.68263 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5320 nv = 96 ne = 84 npr = 26137 no. pairs analyzed = 26137 no. exposed pairs = 1775 no. arc points = 12912 no. surface atoms = 611 nbur = 732 mkacc time = 4.9999997E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 387 mr = 2826 m= 4 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 6.0000002E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1400000 number of dielectric boundary points 2808 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 942 ## 55 charges are in solution ## iepsmp to db, and charging done at 0.2000000 number of grid points assigned charge 5515 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.5571179E-08 3.5917690E-08 midg,1,midg; midg,igrid,midg -8.1589491E-08 9.3171522E-08 1,midg,midg; igrid,midg,midg -1.2504627E-07 1.3961009E-07 gauss-seidel spectral radius is 0.9905685 estimated iterations to convergence 84 setup time was (sec) 0.3100000 now iterating at: 13:59:56 rms-change max change #iterations 0.2055196 35.99497 at 10iterations 2.8021762E-02 4.343325 at 20iterations 3.7814614E-03 0.6212807 at 30iterations 5.0966913E-04 8.6827755E-02 at 40iterations 6.9363770E-05 1.3618469E-02 at 50iterations finished qdiffx linear iterations at : 13:59:59 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 6.9363770E-05 1.3618469E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 13:59:59 3.310u 0.184s 0:03.90 89.4% 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 Mon Oct 10 2011 at 13:59:59 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1343 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.238665 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): -21.62700 21.08400 ymin,ymax (A): -61.17300 -13.46600 zmin,zma (A): 7.414000 45.50500 x,y,z range (A): 42.71100 47.70700 38.09100 scale (grids/A): 2.238665 object centre (A): -0.2715006 -37.31950 26.45950 number of atom coordinates read : 1343 total number of charged atoms : 1273 net assigned charge : -0.4999965 assigned positive charge : 204.5722 centred at (gu) : 92.57788 93.40411 89.25204 assigned negative charge : -205.0722 centred at (gu) : 92.03784 93.04669 89.04815 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 56248 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12912 grid for indexing accessible points = 1.400000 m= 21591 mr = 37837 m= 4993 mr = 16119 m= 624 mr = 3377 m= 30 mr = 352 m= 0 mr = 5 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 25796 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 10144 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) : 0.7462217 object centre at (A) : -0.2715006 -37.31950 26.45950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.6852425E-03 1.6222630E-02 midg,1,midg; midg,igrid,midg -2.4495931E-02 1.3631476E-02 1,midg,midg; igrid,midg,midg -3.2505609E-02 -3.0473392E-03 gauss-seidel spectral radius is 0.9988744 estimated iterations to convergence 236 setup time was (sec) 0.5000000 now iterating at: 14:00:00 rms-change max change #iterations 4.073920 216.4557 at 10iterations 2.047778 82.50339 at 20iterations 1.031123 37.57452 at 30iterations 0.5146034 20.13063 at 40iterations 0.2592507 8.746782 at 50iterations 0.1299226 4.706842 at 60iterations 6.4996019E-02 2.102505 at 70iterations 3.2721374E-02 1.220808 at 80iterations 1.6389281E-02 0.5485535 at 90iterations 8.2163187E-03 0.2682452 at 100iterations 4.1234409E-03 0.1434908 at 110iterations 2.0736638E-03 6.7742348E-02 at 120iterations finished qdiffx linear iterations at : 14:00:07 total time elapsed so far: 7.430000 # loops : 120 mean,max change (kT/e) : 2.0736638E-03 6.7742348E-02 energy calculations done at 7.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.560000 DelPhi exited at 14:00:08 7.565u 0.320s 0:08.28 95.1% 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1343 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.357998 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): -21.62700 21.08400 ymin,ymax (A): -61.17300 -13.46600 zmin,zma (A): 7.414000 45.50500 x,y,z range (A): 42.71100 47.70700 38.09100 scale (grids/A): 3.357998 object centre (A): -0.2715006 -37.31950 26.45950 number of atom coordinates read : 1343 total number of charged atoms : 1273 net assigned charge : -0.4999965 assigned positive charge : 204.5722 centred at (gu) : 93.86691 95.10628 88.87820 assigned negative charge : -205.0722 centred at (gu) : 93.05694 94.57014 88.57228 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 129483 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12912 grid for indexing accessible points = 1.400000 m= 66517 mr = 91393 m= 28391 mr = 54578 m= 9681 mr = 23158 m= 2456 mr = 7535 m= 391 mr = 1790 m= 29 mr = 278 m= 0 mr = 17 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8700000 number of dielectric boundary points 58199 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 10184 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) : 2.238665 object centre at (A) : -0.2715006 -37.31950 26.45950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1855546 0.1279346 midg,1,midg; midg,igrid,midg -0.1893717 1.5982058E-02 1,midg,midg; igrid,midg,midg -0.3040452 -5.3060345E-02 gauss-seidel spectral radius is 0.9993024 estimated iterations to convergence 299 setup time was (sec) 1.090000 now iterating at: 14:00:09 rms-change max change #iterations 8.843965 302.4575 at 10iterations 5.151410 136.0034 at 20iterations 3.019516 64.29149 at 30iterations 1.754048 35.82452 at 40iterations 1.025461 20.59112 at 50iterations 0.5979593 12.08928 at 60iterations 0.3484726 6.506729 at 70iterations 0.2030900 3.847643 at 80iterations 0.1182754 2.515570 at 90iterations 6.8931505E-02 1.364431 at 100iterations 4.0217396E-02 0.7388735 at 110iterations 2.3448450E-02 0.4612274 at 120iterations 1.3673190E-02 0.2611847 at 130iterations 7.9429895E-03 0.1555176 at 140iterations 4.6460140E-03 9.9386215E-02 at 150iterations 2.7000105E-03 5.1685333E-02 at 160iterations 1.5772549E-03 3.0884266E-02 at 170iterations 9.1546786E-04 1.7501831E-02 at 180iterations finished qdiffx linear iterations at : 14:00:20 total time elapsed so far: 11.88000 # loops : 180 mean,max change (kT/e) : 9.1546786E-04 1.7501831E-02 energy calculations done at 11.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.02000 DelPhi exited at 14:00:21 12.020u 0.199s 0:13.17 92.7% 0+0k 0+0io 0pf+0w