Sat Oct 8 14:03:24 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 14:03:24 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: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2993 !!! WARNING: HIR 111 has a net charge of 0.5140 !!! WARNING: GLU 314 has a net charge of -0.2720 !!! WARNING: NDP 319 has a net charge of -3.0000 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: 0.6408179 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): -12.17600 43.37800 ymin,ymax (A): -23.89800 22.51800 zmin,zma (A): -6.577000 47.91600 x,y,z range (A): 55.55400 46.41600 54.49300 scale (grids/A): 0.6408179 object centre (A): 15.60100 -0.6899996 20.66950 number of atom coordinates read : 2993 total number of charged atoms : 2849 net assigned charge : 1.742008 assigned positive charge : 450.2727 centred at (gu) : 88.75064 90.06885 91.26561 assigned negative charge : -448.5313 centred at (gu) : 88.64671 89.92609 91.28686 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8165 nv = 96 ne = 84 npr = 62705 no. pairs analyzed = 62705 no. exposed pairs = 3359 no. arc points = 23764 no. surface atoms = 1153 nbur = 1840 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 411 mr = 4757 m= 0 mr = 43 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3776 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2324 ## 218 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9891 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.4022639E-09 -1.6675714E-10 midg,1,midg; midg,igrid,midg -1.6822369E-08 2.2477762E-08 1,midg,midg; igrid,midg,midg -1.5321110E-08 1.2969227E-08 gauss-seidel spectral radius is 0.9874123 estimated iterations to convergence 73 setup time was (sec) 0.6400000 now iterating at: 14:03:25 rms-change max change #iterations 0.1577251 19.63521 at 10iterations 1.6142167E-02 2.109665 at 20iterations 1.6021474E-03 0.2166519 at 30iterations 1.7105709E-04 2.2857666E-02 at 40iterations 1.9036042E-05 2.6168823E-03 at 50iterations finished qdiffx linear iterations at : 14:03:29 total time elapsed so far: 4.300000 # loops : 50 mean,max change (kT/e) : 1.9036042E-05 2.6168823E-03 energy calculations done at 4.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.460000 DelPhi exited at 14:03:30 4.469u 0.407s 0:05.14 94.5% 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 14:03:30 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: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2993 !!! WARNING: HIR 111 has a net charge of 0.5140 !!! WARNING: GLU 314 has a net charge of -0.2720 !!! WARNING: NDP 319 has a net charge of -3.0000 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: 1.922454 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): -12.17600 43.37800 ymin,ymax (A): -23.89800 22.51800 zmin,zma (A): -6.577000 47.91600 x,y,z range (A): 55.55400 46.41600 54.49300 scale (grids/A): 1.922454 object centre (A): 15.60100 -0.6899996 20.66950 number of atom coordinates read : 2993 total number of charged atoms : 2849 net assigned charge : 1.742008 assigned positive charge : 450.2727 centred at (gu) : 86.25128 90.20580 93.79655 assigned negative charge : -448.5313 centred at (gu) : 85.93957 89.77795 93.86049 start vw surface at 0.1200000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 88573 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23764 grid for indexing accessible points = 1.400000 m= 31552 mr = 63858 m= 4473 mr = 23592 m= 265 mr = 2681 m= 4 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 34644 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 155 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 22462 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) : 0.6408179 object centre at (A) : 15.60100 -0.6899996 20.66950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.6775697E-03 2.4391643E-03 midg,1,midg; midg,igrid,midg -6.1851558E-03 3.1268876E-02 1,midg,midg; igrid,midg,midg -3.6879644E-02 2.9934356E-02 gauss-seidel spectral radius is 0.9986920 estimated iterations to convergence 219 setup time was (sec) 1.030000 now iterating at: 14:03:31 rms-change max change #iterations 4.711353 185.6765 at 10iterations 2.251274 71.01836 at 20iterations 1.071530 32.19862 at 30iterations 0.5108513 15.30753 at 40iterations 0.2439896 7.032242 at 50iterations 0.1158794 3.406261 at 60iterations 5.5262141E-02 1.569314 at 70iterations 2.6402382E-02 0.7691040 at 80iterations 1.2531839E-02 0.3437334 at 90iterations 5.9919264E-03 0.1809444 at 100iterations 2.8485693E-03 8.5325241E-02 at 110iterations 1.3623070E-03 4.2537689E-02 at 120iterations finished qdiffx linear iterations at : 14:03:40 total time elapsed so far: 10.47000 # loops : 120 mean,max change (kT/e) : 1.3623070E-03 4.2537689E-02 energy calculations done at 10.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.65000 DelPhi exited at 14:03:41 10.656u 0.456s 0:11.37 97.6% 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 14:03:41 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: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2993 !!! WARNING: HIR 111 has a net charge of 0.5140 !!! WARNING: GLU 314 has a net charge of -0.2720 !!! WARNING: NDP 319 has a net charge of -3.0000 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: 2.883681 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): -12.17600 43.37800 ymin,ymax (A): -23.89800 22.51800 zmin,zma (A): -6.577000 47.91600 x,y,z range (A): 55.55400 46.41600 54.49300 scale (grids/A): 2.883681 object centre (A): 15.60100 -0.6899996 20.66950 number of atom coordinates read : 2993 total number of charged atoms : 2849 net assigned charge : 1.742008 assigned positive charge : 450.2727 centred at (gu) : 84.37687 90.30875 95.69455 assigned negative charge : -448.5313 centred at (gu) : 83.90940 89.66675 95.79054 start vw surface at 0.1300000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 205358 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23764 grid for indexing accessible points = 1.400000 m= 103696 mr = 154156 m= 35699 mr = 86443 m= 7965 mr = 28627 m= 1121 mr = 5683 m= 62 mr = 724 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 1.120000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.850000 number of dielectric boundary points 78241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 22792 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) : 1.922454 object centre at (A) : 15.60100 -0.6899996 20.66950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5430048E-02 0.1686344 midg,1,midg; midg,igrid,midg -5.7596155E-02 0.3316725 1,midg,midg; igrid,midg,midg -0.5191759 0.3362628 gauss-seidel spectral radius is 0.9992768 estimated iterations to convergence 293 setup time was (sec) 2.170000 now iterating at: 14:03:44 rms-change max change #iterations 10.94025 409.9727 at 10iterations 6.405120 121.7668 at 20iterations 3.726819 79.99982 at 30iterations 2.167256 41.87611 at 40iterations 1.256533 22.56111 at 50iterations 0.7287043 12.17338 at 60iterations 0.4226143 7.076169 at 70iterations 0.2449255 4.207952 at 80iterations 0.1415648 2.335644 at 90iterations 8.1928231E-02 1.381256 at 100iterations 4.7355425E-02 0.8242989 at 110iterations 2.7389241E-02 0.4509239 at 120iterations 1.5859708E-02 0.2598807 at 130iterations 9.1757448E-03 0.1588149 at 140iterations 5.3058625E-03 8.7965012E-02 at 150iterations 3.0721794E-03 4.9806595E-02 at 160iterations 1.7784388E-03 3.1625748E-02 at 170iterations 1.0317586E-03 1.6612053E-02 at 180iterations finished qdiffx linear iterations at : 14:04:00 total time elapsed so far: 18.14000 # loops : 180 mean,max change (kT/e) : 1.0317586E-03 1.6612053E-02 energy calculations done at 18.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.30000 DelPhi exited at 14:04:00 18.308u 0.485s 0:19.06 98.5% 0+0k 0+0io 0pf+0w