Mon Oct 10 14:02:08 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 14:02:08 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2855 !!! WARNING: HIR 209 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: 0.6556531 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): -5.313000 44.80800 ymin,ymax (A): 6.114000 60.41100 zmin,zma (A): -10.11600 43.96100 x,y,z range (A): 50.12100 54.29700 54.07700 scale (grids/A): 0.6556531 object centre (A): 19.74750 33.26250 16.92250 number of atom coordinates read : 2855 total number of charged atoms : 2767 net assigned charge : -4.485964 assigned positive charge : 424.3599 centred at (gu) : 90.96655 91.46942 89.25910 assigned negative charge : -428.8477 centred at (gu) : 90.92799 91.50537 89.17887 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8790 nv = 96 ne = 84 npr = 54803 no. pairs analyzed = 54803 no. exposed pairs = 4020 no. arc points = 28360 no. surface atoms = 1329 nbur = 1526 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 613 mr = 4626 m= 4 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 4684 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2523 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 10045 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.0003076E-08 4.6774904E-09 midg,1,midg; midg,igrid,midg -2.2903097E-09 -2.3027086E-08 1,midg,midg; igrid,midg,midg -1.4315437E-08 -2.8705742E-09 gauss-seidel spectral radius is 0.9879884 estimated iterations to convergence 75 setup time was (sec) 0.4000000 now iterating at: 14:02:09 rms-change max change #iterations 0.1746177 26.50893 at 10iterations 1.8465688E-02 2.705624 at 20iterations 1.9585872E-03 0.2927604 at 30iterations 2.6580409E-04 4.0683746E-02 at 40iterations 6.9549518E-05 1.3097763E-02 at 50iterations finished qdiffx linear iterations at : 14:02:11 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 6.9549518E-05 1.3097763E-02 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 14:02:12 3.354u 0.165s 0:04.24 82.7% 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 14:02:13 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2855 !!! WARNING: HIR 209 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: 1.966959 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): -5.313000 44.80800 ymin,ymax (A): 6.114000 60.41100 zmin,zma (A): -10.11600 43.96100 x,y,z range (A): 50.12100 54.29700 54.07700 scale (grids/A): 1.966959 object centre (A): 19.74750 33.26250 16.92250 number of atom coordinates read : 2855 total number of charged atoms : 2767 net assigned charge : -4.485964 assigned positive charge : 424.3599 centred at (gu) : 92.89870 94.40736 87.77643 assigned negative charge : -428.8477 centred at (gu) : 92.78384 94.51630 87.53644 start vw surface at 0.1100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 93372 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28360 grid for indexing accessible points = 1.400000 m= 35720 mr = 62936 m= 7089 mr = 25819 m= 575 mr = 4581 m= 9 mr = 210 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 198 time to turn everything in is 0.4800000 number of dielectric boundary points 43219 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 105 iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 21886 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) : 0.6556531 object centre at (A) : 19.74750 33.26250 16.92250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3068074E-02 -2.0812543E-02 midg,1,midg; midg,igrid,midg 1.7802978E-03 -3.7172064E-02 1,midg,midg; igrid,midg,midg -1.4420877E-02 1.9378180E-02 gauss-seidel spectral radius is 0.9987713 estimated iterations to convergence 226 setup time was (sec) 0.7100000 now iterating at: 14:02:14 rms-change max change #iterations 4.783864 210.6524 at 10iterations 2.326906 73.94246 at 20iterations 1.129067 34.82273 at 30iterations 0.5500460 16.49147 at 40iterations 0.2674009 8.525284 at 50iterations 0.1301809 3.952370 at 60iterations 6.3241497E-02 1.897362 at 70iterations 3.0868834E-02 0.9041915 at 80iterations 1.5029873E-02 0.4564126 at 90iterations 7.3333969E-03 0.2002172 at 100iterations 3.5797993E-03 0.1002159 at 110iterations 1.7495855E-03 4.7817230E-02 at 120iterations finished qdiffx linear iterations at : 14:02:21 total time elapsed so far: 7.920000 # loops : 120 mean,max change (kT/e) : 1.7495855E-03 4.7817230E-02 energy calculations done at 7.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.050000 DelPhi exited at 14:02:23 8.051u 0.186s 0:10.01 82.2% 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 Mon Oct 10 2011 at 14:02:23 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2855 !!! WARNING: HIR 209 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: 2.950439 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): -5.313000 44.80800 ymin,ymax (A): 6.114000 60.41100 zmin,zma (A): -10.11600 43.96100 x,y,z range (A): 50.12100 54.29700 54.07700 scale (grids/A): 2.950439 object centre (A): 19.74750 33.26250 16.92250 number of atom coordinates read : 2855 total number of charged atoms : 2767 net assigned charge : -4.485964 assigned positive charge : 424.3599 centred at (gu) : 94.34780 96.61080 86.66439 assigned negative charge : -428.8477 centred at (gu) : 94.17573 96.77435 86.30463 start vw surface at 0.1000000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 215492 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28360 grid for indexing accessible points = 1.400000 m= 110885 mr = 153116 m= 45412 mr = 89120 m= 13427 mr = 36223 m= 2388 mr = 10203 m= 181 mr = 1574 m= 4 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 540 time to turn everything in is 1.240000 number of dielectric boundary points 97479 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 22134 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) : 1.966959 object centre at (A) : 19.74750 33.26250 16.92250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8306886E-02 -6.6514678E-02 midg,1,midg; midg,igrid,midg 6.7596622E-02 -0.5985483 1,midg,midg; igrid,midg,midg -0.1872422 0.2387506 gauss-seidel spectral radius is 0.9993145 estimated iterations to convergence 301 setup time was (sec) 1.490000 now iterating at: 14:02:24 rms-change max change #iterations 11.15127 429.0624 at 10iterations 6.678423 143.5069 at 20iterations 3.967671 80.82710 at 30iterations 2.363206 49.35455 at 40iterations 1.397225 25.21942 at 50iterations 0.8269081 14.16789 at 60iterations 0.4874341 8.209038 at 70iterations 0.2877596 4.630058 at 80iterations 0.1694240 2.666686 at 90iterations 9.9783771E-02 1.700043 at 100iterations 5.8626629E-02 0.9274739 at 110iterations 3.4464654E-02 0.6097546 at 120iterations 2.0229515E-02 0.3532439 at 130iterations 1.1893478E-02 0.2174034 at 140iterations 7.0027658E-03 0.1077461 at 150iterations 4.1062511E-03 7.5164795E-02 at 160iterations 2.4207789E-03 3.9672852E-02 at 170iterations 1.4251776E-03 2.6131153E-02 at 180iterations finished qdiffx linear iterations at : 14:02:36 total time elapsed so far: 13.27000 # loops : 180 mean,max change (kT/e) : 1.4251776E-03 2.6131153E-02 energy calculations done at 13.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.39000 DelPhi exited at 14:02:37 13.390u 0.213s 0:14.18 95.9% 0+0k 0+0io 0pf+0w