Sat Oct 8 19:02:34 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 Sat Oct 8 2011 at 19:02:34 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2572 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 439 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: 0.6227587 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): -31.61200 17.44100 ymin,ymax (A): -23.94100 22.82500 zmin,zma (A): -12.40200 44.76300 x,y,z range (A): 49.05300 46.76600 57.16500 scale (grids/A): 0.6227587 object centre (A): -7.085500 -0.5580006 16.18050 number of atom coordinates read : 2572 total number of charged atoms : 2466 net assigned charge : 4.800008 assigned positive charge : 394.0620 centred at (gu) : 88.37829 89.28027 89.87186 assigned negative charge : -389.2625 centred at (gu) : 88.31826 89.33360 89.70594 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6633 nv = 96 ne = 84 npr = 52510 no. pairs analyzed = 52510 no. exposed pairs = 3022 no. arc points = 21835 no. surface atoms = 1015 nbur = 1557 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 334 mr = 3718 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.3000000 number of dielectric boundary points 3210 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2211 ## 254 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8198 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.1330382E-09 1.5542643E-08 midg,1,midg; midg,igrid,midg 9.4589003E-09 3.7654291E-10 1,midg,midg; igrid,midg,midg -2.3524044E-10 6.0315584E-09 gauss-seidel spectral radius is 0.9866424 estimated iterations to convergence 71 setup time was (sec) 0.5700000 now iterating at: 19:02:34 rms-change max change #iterations 0.1325524 20.23040 at 10iterations 1.2246808E-02 1.831032 at 20iterations 1.1332016E-03 0.1733673 at 30iterations 1.0551822E-04 1.5996933E-02 at 40iterations 1.0025783E-05 1.5943050E-03 at 50iterations finished qdiffx linear iterations at : 19:02:38 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 1.0025783E-05 1.5943050E-03 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.230000 DelPhi exited at 19:02:38 4.230u 0.247s 0:04.75 94.1% 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 19:02:38 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2572 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 439 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: 1.868276 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): -31.61200 17.44100 ymin,ymax (A): -23.94100 22.82500 zmin,zma (A): -12.40200 44.76300 x,y,z range (A): 49.05300 46.76600 57.16500 scale (grids/A): 1.868276 object centre (A): -7.085500 -0.5580006 16.18050 number of atom coordinates read : 2572 total number of charged atoms : 2466 net assigned charge : 4.800008 assigned positive charge : 394.0620 centred at (gu) : 85.13413 87.84025 89.61501 assigned negative charge : -389.2625 centred at (gu) : 84.95454 88.00070 89.11759 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 72177 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21835 grid for indexing accessible points = 1.400000 m= 25918 mr = 50655 m= 3798 mr = 19205 m= 200 mr = 2375 m= 4 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 3106 time to turn everything in is 0.5400000 number of dielectric boundary points 29797 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 192 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 19363 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) : 0.6227587 object centre at (A) : -7.085500 -0.5580006 16.18050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9600028E-02 3.3329546E-02 midg,1,midg; midg,igrid,midg 1.2255988E-02 3.3186274E-03 1,midg,midg; igrid,midg,midg -1.3868784E-03 2.7357630E-02 gauss-seidel spectral radius is 0.9985800 estimated iterations to convergence 210 setup time was (sec) 0.8700000 now iterating at: 19:02:40 rms-change max change #iterations 4.079628 205.8406 at 10iterations 1.870488 67.96323 at 20iterations 0.8653651 30.78986 at 30iterations 0.3986852 13.19972 at 40iterations 0.1840227 6.726959 at 50iterations 8.5247025E-02 3.060272 at 60iterations 3.9314672E-02 1.397909 at 70iterations 1.8108118E-02 0.5969276 at 80iterations 8.3403382E-03 0.2838211 at 90iterations 3.8654790E-03 0.1316509 at 100iterations 1.7827322E-03 5.5448532E-02 at 110iterations 8.2382257E-04 2.5864601E-02 at 120iterations finished qdiffx linear iterations at : 19:02:48 total time elapsed so far: 9.570000 # loops : 120 mean,max change (kT/e) : 8.2382257E-04 2.5864601E-02 energy calculations done at 9.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.740000 DelPhi exited at 19:02:49 9.747u 0.279s 0:10.29 97.2% 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 19:02:49 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2572 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 439 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.802414 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): -31.61200 17.44100 ymin,ymax (A): -23.94100 22.82500 zmin,zma (A): -12.40200 44.76300 x,y,z range (A): 49.05300 46.76600 57.16500 scale (grids/A): 2.802414 object centre (A): -7.085500 -0.5580006 16.18050 number of atom coordinates read : 2572 total number of charged atoms : 2466 net assigned charge : 4.800008 assigned positive charge : 394.0620 centred at (gu) : 82.70109 86.76038 89.42245 assigned negative charge : -389.2625 centred at (gu) : 82.43179 87.00108 88.67631 start vw surface at 0.1300000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 166832 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21835 grid for indexing accessible points = 1.400000 m= 84746 mr = 122166 m= 29648 mr = 70088 m= 6817 mr = 23862 m= 976 mr = 5190 m= 45 mr = 683 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.8100001 no. cavity mid-points inaccessible to solvent = 10724 time to turn everything in is 1.460000 number of dielectric boundary points 67068 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 19727 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) : 1.868276 object centre at (A) : -7.085500 -0.5580006 16.18050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1173690 0.3522702 midg,1,midg; midg,igrid,midg 0.1220562 2.3610028E-02 1,midg,midg; igrid,midg,midg -1.4002188E-02 0.3763201 gauss-seidel spectral radius is 0.9992400 estimated iterations to convergence 286 setup time was (sec) 1.810000 now iterating at: 19:02:51 rms-change max change #iterations 9.560635 299.3871 at 10iterations 5.487963 113.9595 at 20iterations 3.133918 64.80836 at 30iterations 1.791173 32.77914 at 40iterations 1.022985 19.13399 at 50iterations 0.5824060 11.48892 at 60iterations 0.3323907 6.304653 at 70iterations 0.1892871 3.573814 at 80iterations 0.1079013 2.029064 at 90iterations 6.1331246E-02 1.090136 at 100iterations 3.4964912E-02 0.6637497 at 110iterations 1.9884907E-02 0.3855438 at 120iterations 1.1333495E-02 0.2120667 at 130iterations 6.4607598E-03 0.1238594 at 140iterations 3.6773270E-03 7.3432922E-02 at 150iterations 2.0947959E-03 3.5919189E-02 at 160iterations 1.1947440E-03 2.2811890E-02 at 170iterations 6.7979662E-04 1.2680054E-02 at 180iterations finished qdiffx linear iterations at : 19:03:05 total time elapsed so far: 15.46000 # loops : 180 mean,max change (kT/e) : 6.7979662E-04 1.2680054E-02 energy calculations done at 15.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.64000 DelPhi exited at 19:03:05 15.644u 0.304s 0:16.21 98.3% 0+0k 0+0io 0pf+0w