Sat Oct 15 15:01:22 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 15:01:22 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2768 !!! WARNING: HIR 121 has a net charge of 0.5140 !!! WARNING: HIR 247 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6094221 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): -10.44800 45.44300 ymin,ymax (A): 30.37000 88.78600 zmin,zma (A): -10.26500 45.56500 x,y,z range (A): 55.89100 58.41599 55.83000 scale (grids/A): 0.6094221 object centre (A): 17.49750 59.57800 17.65000 number of atom coordinates read : 2768 total number of charged atoms : 2629 net assigned charge : -0.4719888 assigned positive charge : 413.3586 centred at (gu) : 89.15692 89.50445 89.51524 assigned negative charge : -413.8317 centred at (gu) : 89.14578 89.48196 89.50006 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6949 nv = 96 ne = 84 npr = 55215 no. pairs analyzed = 55215 no. exposed pairs = 4112 no. arc points = 28989 no. surface atoms = 1348 nbur = 1420 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 392 mr = 3258 m= 4 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 4061 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2848 ## 265 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8548 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1666526E-09 4.7157966E-10 midg,1,midg; midg,igrid,midg -1.5955761E-09 8.0732637E-10 1,midg,midg; igrid,midg,midg -1.0102816E-09 2.6126495E-10 gauss-seidel spectral radius is 0.9860911 estimated iterations to convergence 69 setup time was (sec) 0.4100000 now iterating at: 15:01:22 rms-change max change #iterations 0.1177535 18.75909 at 10iterations 1.0372269E-02 1.463495 at 20iterations 9.6018566E-04 0.1418819 at 30iterations 1.3528758E-04 2.3555756E-02 at 40iterations 3.6748283E-05 7.8291893E-03 at 50iterations finished qdiffx linear iterations at : 15:01:26 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 3.6748283E-05 7.8291893E-03 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 15:01:26 3.526u 0.203s 0:04.72 78.8% 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 15:01:26 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2768 !!! WARNING: HIR 121 has a net charge of 0.5140 !!! WARNING: HIR 247 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.828267 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): -10.44800 45.44300 ymin,ymax (A): 30.37000 88.78600 zmin,zma (A): -10.26500 45.56500 x,y,z range (A): 55.89100 58.41599 55.83000 scale (grids/A): 1.828267 object centre (A): 17.49750 59.57800 17.65000 number of atom coordinates read : 2768 total number of charged atoms : 2629 net assigned charge : -0.4719888 assigned positive charge : 413.3586 centred at (gu) : 87.47028 88.51272 88.54511 assigned negative charge : -413.8317 centred at (gu) : 87.43725 88.44575 88.49998 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 74474 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28989 grid for indexing accessible points = 1.400000 m= 24904 mr = 47414 m= 3655 mr = 16559 m= 171 mr = 1860 m= 4 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 37341 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 149 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 20543 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) : 0.6094221 object centre at (A) : 17.49750 59.57800 17.65000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.5747216E-03 -1.6980343E-02 midg,1,midg; midg,igrid,midg 1.2061856E-02 -6.3251415E-03 1,midg,midg; igrid,midg,midg 1.1073119E-02 4.3569054E-03 gauss-seidel spectral radius is 0.9985658 estimated iterations to convergence 209 setup time was (sec) 0.6400000 now iterating at: 15:01:27 rms-change max change #iterations 4.084941 159.5537 at 10iterations 1.861269 61.71974 at 20iterations 0.8500187 29.00700 at 30iterations 0.3902534 14.42650 at 40iterations 0.1788870 6.431537 at 50iterations 8.1698656E-02 2.559125 at 60iterations 3.7469432E-02 1.288366 at 70iterations 1.7187908E-02 0.5731554 at 80iterations 7.9158610E-03 0.2884541 at 90iterations 3.6205871E-03 0.1151123 at 100iterations 1.6724531E-03 5.4940701E-02 at 110iterations 7.7925914E-04 2.6820183E-02 at 120iterations finished qdiffx linear iterations at : 15:01:35 total time elapsed so far: 8.340000 # loops : 120 mean,max change (kT/e) : 7.7925914E-04 2.6820183E-02 energy calculations done at 8.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.470000 DelPhi exited at 15:01:35 8.474u 0.245s 0:09.01 96.6% 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 15 2011 at 15:01:35 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2768 !!! WARNING: HIR 121 has a net charge of 0.5140 !!! WARNING: HIR 247 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.742400 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): -10.44800 45.44300 ymin,ymax (A): 30.37000 88.78600 zmin,zma (A): -10.26500 45.56500 x,y,z range (A): 55.89100 58.41599 55.83000 scale (grids/A): 2.742400 object centre (A): 17.49750 59.57800 17.65000 number of atom coordinates read : 2768 total number of charged atoms : 2629 net assigned charge : -0.4719888 assigned positive charge : 413.3586 centred at (gu) : 86.20529 87.76898 87.81753 assigned negative charge : -413.8317 centred at (gu) : 86.15591 87.66849 87.74999 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 172442 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28989 grid for indexing accessible points = 1.400000 m= 80365 mr = 116637 m= 27429 mr = 61546 m= 6199 mr = 20314 m= 706 mr = 4059 m= 16 mr = 364 m= 0 mr = 2 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9600000 number of dielectric boundary points 84235 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 21030 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) : 1.828267 object centre at (A) : 17.49750 59.57800 17.65000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1262013 -0.1938379 midg,1,midg; midg,igrid,midg 0.3394212 -2.5559673E-02 1,midg,midg; igrid,midg,midg 0.2739355 1.5041876E-02 gauss-seidel spectral radius is 0.9992622 estimated iterations to convergence 291 setup time was (sec) 1.230000 now iterating at: 15:01:38 rms-change max change #iterations 10.00664 325.4794 at 10iterations 5.953526 162.3821 at 20iterations 3.506607 81.87286 at 30iterations 2.044058 46.35472 at 40iterations 1.193206 24.34427 at 50iterations 0.6935772 15.90373 at 60iterations 0.4017040 7.930907 at 70iterations 0.2319630 4.207016 at 80iterations 0.1343366 2.509321 at 90iterations 7.7680290E-02 1.516461 at 100iterations 4.4733990E-02 0.9311309 at 110iterations 2.5790552E-02 0.4672496 at 120iterations 1.4893483E-02 0.2740726 at 130iterations 8.6066956E-03 0.1705803 at 140iterations 4.9835029E-03 8.8880539E-02 at 150iterations 2.9159479E-03 5.6405067E-02 at 160iterations 1.7210235E-03 3.2606125E-02 at 170iterations 1.0400021E-03 2.1119118E-02 at 180iterations finished qdiffx linear iterations at : 15:01:54 total time elapsed so far: 13.56000 # loops : 180 mean,max change (kT/e) : 1.0400021E-03 2.1119118E-02 energy calculations done at 13.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.70000 DelPhi exited at 15:01:55 13.698u 0.361s 0:19.33 72.6% 0+0k 0+0io 0pf+0w