Sat Oct 8 18:49:06 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 8 2011 at 18:49:06 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 = 2594 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6330014 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): -32.12900 17.55500 ymin,ymax (A): -22.81300 23.94100 zmin,zma (A): -12.15800 44.08200 x,y,z range (A): 49.68400 46.75400 56.24000 scale (grids/A): 0.6330014 object centre (A): -7.286999 0.5640001 15.96200 number of atom coordinates read : 2594 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 392.6040 centred at (gu) : 88.54846 88.66521 89.96863 assigned negative charge : -388.6046 centred at (gu) : 88.45826 88.70950 89.84473 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6863 nv = 96 ne = 84 npr = 54555 no. pairs analyzed = 54555 no. exposed pairs = 3015 no. arc points = 21529 no. surface atoms = 1030 nbur = 1564 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 368 mr = 3855 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 47 time to turn everything in is 0.3600000 number of dielectric boundary points 3331 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2152 ## 197 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8364 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.2706858E-09 1.6438369E-08 midg,1,midg; midg,igrid,midg 1.2080789E-08 4.7410481E-10 1,midg,midg; igrid,midg,midg -5.5156923E-09 9.8140545E-09 gauss-seidel spectral radius is 0.9870663 estimated iterations to convergence 72 setup time was (sec) 0.6300000 now iterating at: 18:49:07 rms-change max change #iterations 0.1395593 19.04035 at 10iterations 1.3680754E-02 1.983208 at 20iterations 1.3571340E-03 0.2294960 at 30iterations 1.4678955E-04 1.9594193E-02 at 40iterations 1.7662549E-05 2.9964447E-03 at 50iterations finished qdiffx linear iterations at : 18:49:10 total time elapsed so far: 4.040000 # loops : 50 mean,max change (kT/e) : 1.7662549E-05 2.9964447E-03 energy calculations done at 4.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.220000 DelPhi exited at 18:49:11 4.222u 0.253s 0:04.74 94.3% 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 Sat Oct 8 2011 at 18:49:11 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 = 2594 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.899004 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): -32.12900 17.55500 ymin,ymax (A): -22.81300 23.94100 zmin,zma (A): -12.15800 44.08200 x,y,z range (A): 49.68400 46.75400 56.24000 scale (grids/A): 1.899004 object centre (A): -7.286999 0.5640001 15.96200 number of atom coordinates read : 2594 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 392.6040 centred at (gu) : 85.64491 85.99510 89.90550 assigned negative charge : -388.6046 centred at (gu) : 85.37463 86.12832 89.53419 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 73610 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21529 grid for indexing accessible points = 1.400000 m= 26766 mr = 51766 m= 3987 mr = 19783 m= 233 mr = 2523 m= 4 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 160 time to turn everything in is 0.5800000 number of dielectric boundary points 30453 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 177 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 19310 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) : 0.6330014 object centre at (A) : -7.286999 0.5640001 15.96200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0330299E-02 2.7612975E-02 midg,1,midg; midg,igrid,midg 1.3982003E-02 2.7661347E-03 1,midg,midg; igrid,midg,midg -2.7060271E-03 3.3554267E-02 gauss-seidel spectral radius is 0.9986207 estimated iterations to convergence 213 setup time was (sec) 0.9000000 now iterating at: 18:49:12 rms-change max change #iterations 4.234706 195.6024 at 10iterations 1.972603 67.55997 at 20iterations 0.9231945 28.83167 at 30iterations 0.4297052 15.89023 at 40iterations 0.2007697 6.907732 at 50iterations 9.4114453E-02 3.352676 at 60iterations 4.3867994E-02 1.333162 at 70iterations 2.0432211E-02 0.7342148 at 80iterations 9.5606521E-03 0.3106384 at 90iterations 4.4702156E-03 0.1576443 at 100iterations 2.0902473E-03 7.6927185E-02 at 110iterations 9.7637915E-04 3.0405045E-02 at 120iterations finished qdiffx linear iterations at : 18:49:20 total time elapsed so far: 9.300000 # loops : 120 mean,max change (kT/e) : 9.7637915E-04 3.0405045E-02 energy calculations done at 9.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.520000 DelPhi exited at 18:49:21 9.525u 0.287s 0:10.09 97.1% 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 Sat Oct 8 2011 at 18:49:21 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 = 2594 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 556 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.848506 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): -32.12900 17.55500 ymin,ymax (A): -22.81300 23.94100 zmin,zma (A): -12.15800 44.08200 x,y,z range (A): 49.68400 46.75400 56.24000 scale (grids/A): 2.848506 object centre (A): -7.286999 0.5640001 15.96200 number of atom coordinates read : 2594 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 392.6040 centred at (gu) : 83.46730 83.99255 89.85808 assigned negative charge : -388.6046 centred at (gu) : 83.06187 84.19245 89.30131 start vw surface at 0.1800000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 170001 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21529 grid for indexing accessible points = 1.400000 m= 86635 mr = 124562 m= 30821 mr = 71545 m= 7264 mr = 24751 m= 1124 mr = 5495 m= 74 mr = 789 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 656 time to turn everything in is 1.570000 number of dielectric boundary points 68750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 19631 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) : 1.899004 object centre at (A) : -7.286999 0.5640001 15.96200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1596944 0.2753476 midg,1,midg; midg,igrid,midg 0.1707756 6.0439617E-03 1,midg,midg; igrid,midg,midg 1.5095670E-02 0.3866872 gauss-seidel spectral radius is 0.9992484 estimated iterations to convergence 288 setup time was (sec) 1.930000 now iterating at: 18:49:23 rms-change max change #iterations 9.836176 369.7994 at 10iterations 5.691763 148.1500 at 20iterations 3.285049 78.87573 at 30iterations 1.885151 47.61794 at 40iterations 1.083366 20.42129 at 50iterations 0.6211976 12.42868 at 60iterations 0.3565467 7.020069 at 70iterations 0.2044292 3.564334 at 80iterations 0.1171133 2.337721 at 90iterations 6.7105852E-02 1.224873 at 100iterations 3.8458902E-02 0.7716599 at 110iterations 2.1975771E-02 0.3814354 at 120iterations 1.2610724E-02 0.2542191 at 130iterations 7.2501991E-03 0.1321077 at 140iterations 4.1800248E-03 8.0032349E-02 at 150iterations 2.4164906E-03 4.7893524E-02 at 160iterations 1.4075655E-03 2.8810501E-02 at 170iterations 8.2777755E-04 1.6799927E-02 at 180iterations finished qdiffx linear iterations at : 18:49:36 total time elapsed so far: 15.19000 # loops : 180 mean,max change (kT/e) : 8.2777755E-04 1.6799927E-02 energy calculations done at 15.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.42000 DelPhi exited at 18:49:37 15.418u 0.264s 0:15.95 98.2% 0+0k 0+0io 0pf+0w