Mon Oct 10 19:36:53 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 19:36:53 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2877 !!! WARNING: LEU 314 has a net charge of -0.0260 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6130849 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): -33.97900 20.94600 ymin,ymax (A): 40.68100 89.58300 zmin,zma (A): 0.2960000 58.36300 x,y,z range (A): 54.92500 48.90200 58.06700 scale (grids/A): 0.6130849 object centre (A): -6.516500 65.13200 29.32950 number of atom coordinates read : 2877 total number of charged atoms : 2734 net assigned charge : 0.4740128 assigned positive charge : 428.2802 centred at (gu) : 92.00891 89.97344 89.09197 assigned negative charge : -427.8069 centred at (gu) : 91.93168 90.05555 89.08887 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7119 nv = 96 ne = 84 npr = 57437 no. pairs analyzed = 57437 no. exposed pairs = 4118 no. arc points = 28128 no. surface atoms = 1358 nbur = 1519 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 370 mr = 3530 m= 0 mr = 33 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3926 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2640 ## 241 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8818 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3125762E-11 3.2184846E-10 midg,1,midg; midg,igrid,midg 5.0791509E-09 -4.6970872E-09 1,midg,midg; igrid,midg,midg -2.8191891E-09 7.5440791E-09 gauss-seidel spectral radius is 0.9862545 estimated iterations to convergence 70 setup time was (sec) 0.6400000 now iterating at: 19:36:54 rms-change max change #iterations 0.1204086 18.43189 at 10iterations 1.0831784E-02 1.713767 at 20iterations 1.0305286E-03 0.1390762 at 30iterations 1.2378029E-04 2.0248413E-02 at 40iterations 2.4825085E-05 5.0477982E-03 at 50iterations finished qdiffx linear iterations at : 19:36:57 total time elapsed so far: 3.910000 # loops : 50 mean,max change (kT/e) : 2.4825085E-05 5.0477982E-03 energy calculations done at 3.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 19:36:58 4.087u 0.269s 0:04.88 88.9% 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 19:36:58 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2877 !!! WARNING: LEU 314 has a net charge of -0.0260 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.839255 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): -33.97900 20.94600 ymin,ymax (A): 40.68100 89.58300 zmin,zma (A): 0.2960000 58.36300 x,y,z range (A): 54.92500 48.90200 58.06700 scale (grids/A): 1.839255 object centre (A): -6.516500 65.13200 29.32950 number of atom coordinates read : 2877 total number of charged atoms : 2734 net assigned charge : 0.4740128 assigned positive charge : 428.2802 centred at (gu) : 96.02592 89.91970 87.27514 assigned negative charge : -427.8069 centred at (gu) : 95.79477 90.16610 87.26601 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 76342 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28128 grid for indexing accessible points = 1.400000 m= 25866 mr = 49909 m= 3987 mr = 17684 m= 229 mr = 2203 m= 2 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 296 time to turn everything in is 0.7000000 number of dielectric boundary points 36577 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 21393 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) : 0.6130849 object centre at (A) : -6.516500 65.13200 29.32950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2786926E-02 -5.5220269E-02 midg,1,midg; midg,igrid,midg 6.2592775E-03 -6.3902780E-04 1,midg,midg; igrid,midg,midg -2.1024002E-02 1.1366290E-02 gauss-seidel spectral radius is 0.9985749 estimated iterations to convergence 210 setup time was (sec) 1.000000 now iterating at: 19:36:59 rms-change max change #iterations 4.189370 189.7156 at 10iterations 1.921500 65.87788 at 20iterations 0.8811157 28.21231 at 30iterations 0.4056985 13.07676 at 40iterations 0.1865114 5.951982 at 50iterations 8.5859790E-02 2.643136 at 60iterations 3.9414551E-02 1.334353 at 70iterations 1.8132396E-02 0.5907383 at 80iterations 8.3401930E-03 0.2609248 at 90iterations 3.8519916E-03 0.1322145 at 100iterations 1.7791261E-03 5.9223175E-02 at 110iterations 8.1912533E-04 2.7009964E-02 at 120iterations finished qdiffx linear iterations at : 19:37:07 total time elapsed so far: 9.350000 # loops : 120 mean,max change (kT/e) : 8.1912533E-04 2.7009964E-02 energy calculations done at 9.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.530000 DelPhi exited at 19:37:08 9.533u 0.283s 0:10.17 96.4% 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 19:37:08 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2877 !!! WARNING: LEU 314 has a net charge of -0.0260 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.758882 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): -33.97900 20.94600 ymin,ymax (A): 40.68100 89.58300 zmin,zma (A): 0.2960000 58.36300 x,y,z range (A): 54.92500 48.90200 58.06700 scale (grids/A): 2.758882 object centre (A): -6.516500 65.13200 29.32950 number of atom coordinates read : 2877 total number of charged atoms : 2734 net assigned charge : 0.4740128 assigned positive charge : 428.2802 centred at (gu) : 99.03869 89.87928 85.91251 assigned negative charge : -427.8069 centred at (gu) : 98.69203 90.24905 85.89886 start vw surface at 0.1500000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 176766 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28128 grid for indexing accessible points = 1.400000 m= 84060 mr = 122703 m= 29508 mr = 64947 m= 6813 mr = 22515 m= 920 mr = 4778 m= 37 mr = 482 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 867 time to turn everything in is 1.760000 number of dielectric boundary points 82678 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 21865 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) : 1.839255 object centre at (A) : -6.516500 65.13200 29.32950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4887989 -0.9565278 midg,1,midg; midg,igrid,midg 5.6979444E-02 -1.5009183E-02 1,midg,midg; igrid,midg,midg -0.1426084 0.1927808 gauss-seidel spectral radius is 0.9992602 estimated iterations to convergence 290 setup time was (sec) 2.090000 now iterating at: 19:37:10 rms-change max change #iterations 10.27582 345.1799 at 10iterations 6.124918 158.3919 at 20iterations 3.617774 77.49660 at 30iterations 2.117307 45.46026 at 40iterations 1.235343 25.42570 at 50iterations 0.7193188 15.55521 at 60iterations 0.4167840 8.213237 at 70iterations 0.2414230 4.405403 at 80iterations 0.1399532 2.775043 at 90iterations 8.0535583E-02 1.496597 at 100iterations 4.6548098E-02 0.9479051 at 110iterations 2.6823901E-02 0.5027270 at 120iterations 1.5457370E-02 0.3044219 at 130iterations 8.9078303E-03 0.1667681 at 140iterations 5.1242122E-03 9.2763901E-02 at 150iterations 2.9517964E-03 5.5425644E-02 at 160iterations 1.6991487E-03 3.0559540E-02 at 170iterations 9.7803259E-04 1.8566132E-02 at 180iterations finished qdiffx linear iterations at : 19:37:24 total time elapsed so far: 15.95000 # loops : 180 mean,max change (kT/e) : 9.7803259E-04 1.8566132E-02 energy calculations done at 15.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.13000 DelPhi exited at 19:37:25 16.131u 0.320s 0:17.22 95.5% 0+0k 0+0io 0pf+0w