Fri Nov 4 20:45:02 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 Fri Nov 4 2011 at 20:45:09 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 ! Automatically converted by prot2crg.py # of charge parameter records: 1082 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2782 !!! WARNING: PTR 161 has a net charge of -2.0000 !!! WARNING: PTR 162 has a net charge of -2.0000 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: 0.5940464 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): 82.28600 142.2140 ymin,ymax (A): 40.67000 95.35500 zmin,zma (A): -26.41200 27.75200 x,y,z range (A): 59.92799 54.68499 54.16400 scale (grids/A): 0.5940464 object centre (A): 112.2500 68.01250 0.6699991 number of atom coordinates read : 2782 total number of charged atoms : 2636 net assigned charge : -2.999983 assigned positive charge : 419.8685 centred at (gu) : 89.28838 90.60126 90.70058 assigned negative charge : -422.8693 centred at (gu) : 89.29302 90.54391 90.59225 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6481 nv = 96 ne = 84 npr = 55912 no. pairs analyzed = 55912 no. exposed pairs = 3594 no. arc points = 25513 no. surface atoms = 1206 nbur = 1576 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 296 mr = 3393 m= 5 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3359 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2660 ## 295 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8270 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.0124855E-09 2.8768616E-09 midg,1,midg; midg,igrid,midg -2.6146882E-09 9.1098912E-10 1,midg,midg; igrid,midg,midg -1.1026293E-09 -1.0657518E-09 gauss-seidel spectral radius is 0.9853524 estimated iterations to convergence 68 setup time was (sec) 0.4100000 now iterating at: 20:45:10 rms-change max change #iterations 0.1042627 18.97642 at 10iterations 8.8719195E-03 1.366100 at 20iterations 1.0452230E-03 0.1647701 at 30iterations 2.6186340E-04 4.9299240E-02 at 40iterations 8.5334948E-05 1.6075134E-02 at 50iterations finished qdiffx linear iterations at : 20:45:13 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 8.5334948E-05 1.6075134E-02 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 20:45:14 3.417u 0.247s 0:06.81 53.5% 0+0k 0+0io 1pf+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 Fri Nov 4 2011 at 20:45:17 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 ! Automatically converted by prot2crg.py # of charge parameter records: 1082 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2782 !!! WARNING: PTR 161 has a net charge of -2.0000 !!! WARNING: PTR 162 has a net charge of -2.0000 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: 1.782139 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): 82.28600 142.2140 ymin,ymax (A): 40.67000 95.35500 zmin,zma (A): -26.41200 27.75200 x,y,z range (A): 59.92799 54.68499 54.16400 scale (grids/A): 1.782139 object centre (A): 112.2500 68.01250 0.6699991 number of atom coordinates read : 2782 total number of charged atoms : 2636 net assigned charge : -2.999983 assigned positive charge : 419.8685 centred at (gu) : 87.86417 91.80310 92.10113 assigned negative charge : -422.8693 centred at (gu) : 87.87878 91.63144 91.77666 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 71655 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25513 grid for indexing accessible points = 1.400000 m= 23449 mr = 49014 m= 3048 mr = 16306 m= 176 mr = 1624 m= 1 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 490 time to turn everything in is 0.3500000 number of dielectric boundary points 31334 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 226 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 20529 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) : 0.5940464 object centre at (A) : 112.2500 68.01250 0.6699991 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0403305E-02 9.4436193E-03 midg,1,midg; midg,igrid,midg -1.2001758E-02 3.0009807E-03 1,midg,midg; igrid,midg,midg -4.3722078E-02 -6.1464249E-03 gauss-seidel spectral radius is 0.9984633 estimated iterations to convergence 202 setup time was (sec) 0.5800000 now iterating at: 20:45:19 rms-change max change #iterations 3.928734 199.8896 at 10iterations 1.753789 82.41047 at 20iterations 0.7815067 30.18002 at 30iterations 0.3502673 11.32041 at 40iterations 0.1567317 5.605598 at 50iterations 7.0038162E-02 2.246443 at 60iterations 3.1419914E-02 1.055192 at 70iterations 1.4124610E-02 0.5071578 at 80iterations 6.3790763E-03 0.2077522 at 90iterations 2.9274235E-03 0.1030011 at 100iterations 1.3732581E-03 4.8123837E-02 at 110iterations 6.8433629E-04 2.4978638E-02 at 120iterations finished qdiffx linear iterations at : 20:45:26 total time elapsed so far: 7.700000 # loops : 120 mean,max change (kT/e) : 6.8433629E-04 2.4978638E-02 energy calculations done at 7.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 20:45:27 7.837u 0.234s 0:10.44 77.2% 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 Fri Nov 4 2011 at 20:45:29 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 ! Automatically converted by prot2crg.py # of charge parameter records: 1082 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2782 !!! WARNING: PTR 161 has a net charge of -2.0000 !!! WARNING: PTR 162 has a net charge of -2.0000 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: 2.673208 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): 82.28600 142.2140 ymin,ymax (A): 40.67000 95.35500 zmin,zma (A): -26.41200 27.75200 x,y,z range (A): 59.92799 54.68499 54.16400 scale (grids/A): 2.673208 object centre (A): 112.2500 68.01250 0.6699991 number of atom coordinates read : 2782 total number of charged atoms : 2636 net assigned charge : -2.999983 assigned positive charge : 419.8685 centred at (gu) : 86.79614 92.70454 93.15155 assigned negative charge : -422.8693 centred at (gu) : 86.81813 92.44713 92.66494 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 166051 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25513 grid for indexing accessible points = 1.400000 m= 79332 mr = 119574 m= 24722 mr = 63325 m= 5277 mr = 18545 m= 676 mr = 3539 m= 28 mr = 404 m= 0 mr = 5 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 1531 time to turn everything in is 0.9000000 number of dielectric boundary points 70694 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 21077 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) : 1.782139 object centre at (A) : 112.2500 68.01250 0.6699991 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4590603 0.1073373 midg,1,midg; midg,igrid,midg -0.1705064 8.4827237E-02 1,midg,midg; igrid,midg,midg -1.094085 -2.2159699E-02 gauss-seidel spectral radius is 0.9992216 estimated iterations to convergence 283 setup time was (sec) 1.150000 now iterating at: 20:45:30 rms-change max change #iterations 9.633685 444.2622 at 10iterations 5.636158 171.6855 at 20iterations 3.261335 79.83956 at 30iterations 1.876597 45.53538 at 40iterations 1.075535 25.34879 at 50iterations 0.6173634 13.17012 at 60iterations 0.3513249 8.564790 at 70iterations 0.2008972 3.841660 at 80iterations 0.1141592 2.227370 at 90iterations 6.5092303E-02 1.378525 at 100iterations 3.6924236E-02 0.7822437 at 110iterations 2.0992609E-02 0.4147644 at 120iterations 1.1929519E-02 0.2351418 at 130iterations 6.7852102E-03 0.1295300 at 140iterations 3.8604077E-03 7.4419022E-02 at 150iterations 2.2113950E-03 4.5448303E-02 at 160iterations 1.2757902E-03 2.5834799E-02 at 170iterations 7.4780447E-04 1.6012192E-02 at 180iterations finished qdiffx linear iterations at : 20:45:42 total time elapsed so far: 12.48000 # loops : 180 mean,max change (kT/e) : 7.4780447E-04 1.6012192E-02 energy calculations done at 12.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.61000 DelPhi exited at 20:45:42 12.608u 0.283s 0:13.79 93.4% 0+0k 0+0io 0pf+0w