Mon Oct 10 10:24:07 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 Mon Oct 10 2011 at 10:24:07 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2678 !!! WARNING: HIT 236 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5855359 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): -20.26900 40.53000 ymin,ymax (A): -11.53400 43.67100 zmin,zma (A): -1.487000 51.45400 x,y,z range (A): 60.79900 55.20500 52.94100 scale (grids/A): 0.5855359 object centre (A): 10.13050 16.06850 24.98350 number of atom coordinates read : 2678 total number of charged atoms : 2533 net assigned charge : 9.014017 assigned positive charge : 394.0932 centred at (gu) : 91.50343 91.34855 86.50645 assigned negative charge : -385.0796 centred at (gu) : 91.67031 91.31772 86.39661 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6169 nv = 96 ne = 84 npr = 52055 no. pairs analyzed = 52055 no. exposed pairs = 3965 no. arc points = 28185 no. surface atoms = 1315 nbur = 1363 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 307 mr = 2812 m= 0 mr = 13 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3651 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2761 ## 297 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7691 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2645465E-10 2.2340838E-09 midg,1,midg; midg,igrid,midg 1.3385598E-09 4.3307722E-09 1,midg,midg; igrid,midg,midg 4.3568678E-09 -1.9457387E-09 gauss-seidel spectral radius is 0.9849326 estimated iterations to convergence 67 setup time was (sec) 0.4000000 now iterating at: 10:24:08 rms-change max change #iterations 9.9644803E-02 18.58716 at 10iterations 7.7238022E-03 1.178535 at 20iterations 6.2732800E-04 0.1120453 at 30iterations 5.7337078E-05 8.4400177E-03 at 40iterations 7.8945832E-06 9.7155571E-04 at 50iterations finished qdiffx linear iterations at : 10:24:11 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 7.8945832E-06 9.7155571E-04 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 10:24:11 3.414u 0.169s 0:03.85 92.7% 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 10:24:11 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2678 !!! WARNING: HIT 236 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.756608 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): -20.26900 40.53000 ymin,ymax (A): -11.53400 43.67100 zmin,zma (A): -1.487000 51.45400 x,y,z range (A): 60.79900 55.20500 52.94100 scale (grids/A): 1.756608 object centre (A): 10.13050 16.06850 24.98350 number of atom coordinates read : 2678 total number of charged atoms : 2533 net assigned charge : 9.014017 assigned positive charge : 394.0932 centred at (gu) : 94.50996 94.04538 79.51920 assigned negative charge : -385.0796 centred at (gu) : 95.01071 93.95283 79.18956 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 66396 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28185 grid for indexing accessible points = 1.400000 m= 21123 mr = 41524 m= 2693 mr = 13700 m= 100 mr = 1297 m= 3 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 236 time to turn everything in is 0.3400000 number of dielectric boundary points 33782 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 227 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 19685 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) : 0.5855359 object centre at (A) : 10.13050 16.06850 24.98350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4567776E-03 7.4420366E-03 midg,1,midg; midg,igrid,midg 1.9400768E-02 2.6421962E-02 1,midg,midg; igrid,midg,midg 1.7045693E-02 1.1617928E-02 gauss-seidel spectral radius is 0.9984138 estimated iterations to convergence 199 setup time was (sec) 0.5600000 now iterating at: 10:24:12 rms-change max change #iterations 3.615858 162.4261 at 10iterations 1.581904 56.01801 at 20iterations 0.6972353 25.09803 at 30iterations 0.3070370 10.14524 at 40iterations 0.1354204 5.092089 at 50iterations 5.9250232E-02 1.993261 at 60iterations 2.6202647E-02 0.9813309 at 70iterations 1.1529256E-02 0.3975296 at 80iterations 5.0646472E-03 0.1779404 at 90iterations 2.2389139E-03 7.9118729E-02 at 100iterations 9.8815339E-04 3.4492493E-02 at 110iterations 4.3616959E-04 1.5472412E-02 at 120iterations finished qdiffx linear iterations at : 10:24:19 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 4.3616959E-04 1.5472412E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 10:24:20 7.778u 0.191s 0:08.24 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 Mon Oct 10 2011 at 10:24:20 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2678 !!! WARNING: HIT 236 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.634912 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): -20.26900 40.53000 ymin,ymax (A): -11.53400 43.67100 zmin,zma (A): -1.487000 51.45400 x,y,z range (A): 60.79900 55.20500 52.94100 scale (grids/A): 2.634912 object centre (A): 10.13050 16.06850 24.98350 number of atom coordinates read : 2678 total number of charged atoms : 2533 net assigned charge : 9.014017 assigned positive charge : 394.0932 centred at (gu) : 96.76483 96.06808 74.27872 assigned negative charge : -385.0796 centred at (gu) : 97.51596 95.92932 73.78436 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 153479 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28185 grid for indexing accessible points = 1.400000 m= 69515 mr = 102089 m= 22521 mr = 52591 m= 4374 mr = 16387 m= 384 mr = 2772 m= 8 mr = 155 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 845 time to turn everything in is 0.8400000 number of dielectric boundary points 76287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 20261 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) : 1.756608 object centre at (A) : 10.13050 16.06850 24.98350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6759596E-02 7.8995846E-02 midg,1,midg; midg,igrid,midg 0.3585572 0.3130355 1,midg,midg; igrid,midg,midg 0.1777841 0.2315114 gauss-seidel spectral radius is 0.9992105 estimated iterations to convergence 281 setup time was (sec) 1.080000 now iterating at: 10:24:21 rms-change max change #iterations 9.226582 323.1196 at 10iterations 5.416461 151.8017 at 20iterations 3.153822 88.82112 at 30iterations 1.820500 48.32369 at 40iterations 1.041785 25.60302 at 50iterations 0.5957648 17.82003 at 60iterations 0.3390952 9.051657 at 70iterations 0.1928483 4.341566 at 80iterations 0.1094959 2.805778 at 90iterations 6.1961770E-02 1.370115 at 100iterations 3.5207234E-02 0.7765460 at 110iterations 1.9902624E-02 0.4240219 at 120iterations 1.1240161E-02 0.2756386 at 130iterations 6.3619083E-03 0.1271814 at 140iterations 3.5877773E-03 7.1587086E-02 at 150iterations 2.0212512E-03 5.1929474E-02 at 160iterations 1.1422912E-03 2.3037434E-02 at 170iterations 6.4483186E-04 1.5514374E-02 at 180iterations finished qdiffx linear iterations at : 10:24:32 total time elapsed so far: 12.39000 # loops : 180 mean,max change (kT/e) : 6.4483186E-04 1.5514374E-02 energy calculations done at 12.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.52000 DelPhi exited at 10:24:33 12.525u 0.201s 0:12.98 97.9% 0+0k 0+0io 0pf+0w