Mon Oct 10 09:54:10 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 09:54:10 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2764 !!! WARNING: HIT 225 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5802487 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): -16.58700 36.28600 ymin,ymax (A): -64.25800 -4.727000 zmin,zma (A): -4.461000 56.89200 x,y,z range (A): 52.87300 59.53100 61.35300 scale (grids/A): 0.5802487 object centre (A): 9.849500 -34.49250 26.21550 number of atom coordinates read : 2764 total number of charged atoms : 2615 net assigned charge : 2.014012 assigned positive charge : 404.9450 centred at (gu) : 88.72315 89.46543 87.66940 assigned negative charge : -402.9314 centred at (gu) : 88.85957 89.40310 87.53510 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6405 nv = 96 ne = 84 npr = 52965 no. pairs analyzed = 52965 no. exposed pairs = 4309 no. arc points = 31283 no. surface atoms = 1407 nbur = 1357 mkacc time = 0.1200000 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 = 1.484000 m= 298 mr = 2795 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3200000 number of dielectric boundary points 3893 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3017 ## 310 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7943 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9545749E-09 1.8108524E-09 midg,1,midg; midg,igrid,midg -8.7659446E-10 1.5142578E-09 1,midg,midg; igrid,midg,midg 4.2824055E-09 -1.6811548E-09 gauss-seidel spectral radius is 0.9846714 estimated iterations to convergence 66 setup time was (sec) 0.5900000 now iterating at: 09:54:11 rms-change max change #iterations 9.2337817E-02 14.87010 at 10iterations 7.2461180E-03 1.324902 at 20iterations 5.5176421E-04 8.4501266E-02 at 30iterations 4.2867439E-05 6.7067146E-03 at 40iterations 3.5749586E-06 5.5885315E-04 at 50iterations finished qdiffx linear iterations at : 09:54:14 total time elapsed so far: 4.000000 # loops : 50 mean,max change (kT/e) : 3.5749586E-06 5.5885315E-04 energy calculations done at 4.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 09:54:14 4.177u 0.219s 0:04.66 93.9% 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 09:54:14 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2764 !!! WARNING: HIT 225 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.740746 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): -16.58700 36.28600 ymin,ymax (A): -64.25800 -4.727000 zmin,zma (A): -4.461000 56.89200 x,y,z range (A): 52.87300 59.53100 61.35300 scale (grids/A): 1.740746 object centre (A): 9.849500 -34.49250 26.21550 number of atom coordinates read : 2764 total number of charged atoms : 2615 net assigned charge : 2.014012 assigned positive charge : 404.9450 centred at (gu) : 86.16865 88.39581 83.00803 assigned negative charge : -402.9314 centred at (gu) : 86.57848 88.20892 82.60502 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 67739 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31283 grid for indexing accessible points = 1.400000 m= 21861 mr = 41179 m= 2819 mr = 13942 m= 141 mr = 1242 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 243 time to turn everything in is 0.5100000 number of dielectric boundary points 36181 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 267 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 20305 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) : 0.5802487 object centre at (A) : 9.849500 -34.49250 26.21550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3977702E-02 2.2848900E-03 midg,1,midg; midg,igrid,midg 1.6233949E-02 2.9917711E-02 1,midg,midg; igrid,midg,midg 1.8444803E-02 -1.0147832E-03 gauss-seidel spectral radius is 0.9984105 estimated iterations to convergence 199 setup time was (sec) 0.8300000 now iterating at: 09:54:16 rms-change max change #iterations 3.654233 170.1504 at 10iterations 1.604527 61.03014 at 20iterations 0.7082483 31.95018 at 30iterations 0.3134783 10.44217 at 40iterations 0.1372515 5.041517 at 50iterations 6.0770277E-02 2.347460 at 60iterations 2.6727322E-02 0.9239388 at 70iterations 1.1787344E-02 0.4523649 at 80iterations 5.1776725E-03 0.1819801 at 90iterations 2.2890945E-03 0.1059875 at 100iterations 1.0094196E-03 3.6259890E-02 at 110iterations 4.4566288E-04 1.5991509E-02 at 120iterations finished qdiffx linear iterations at : 09:54:24 total time elapsed so far: 9.310000 # loops : 120 mean,max change (kT/e) : 4.4566288E-04 1.5991509E-02 energy calculations done at 9.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.500000 DelPhi exited at 09:54:25 9.499u 0.279s 0:10.04 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 Mon Oct 10 2011 at 09:54:25 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2764 !!! WARNING: HIT 225 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.611119 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): -16.58700 36.28600 ymin,ymax (A): -64.25800 -4.727000 zmin,zma (A): -4.461000 56.89200 x,y,z range (A): 52.87300 59.53100 61.35300 scale (grids/A): 2.611119 object centre (A): 9.849500 -34.49250 26.21550 number of atom coordinates read : 2764 total number of charged atoms : 2615 net assigned charge : 2.014012 assigned positive charge : 404.9450 centred at (gu) : 84.25304 87.59363 79.51190 assigned negative charge : -402.9314 centred at (gu) : 84.86765 87.31331 78.90735 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 156470 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31283 grid for indexing accessible points = 1.400000 m= 71155 mr = 101870 m= 23564 mr = 52865 m= 4399 mr = 16851 m= 425 mr = 2590 m= 15 mr = 172 m= 0 mr = 0 time to grow re-entrant surface = 0.7599999 no. cavity mid-points inaccessible to solvent = 840 time to turn everything in is 1.320000 number of dielectric boundary points 81680 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 20915 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) : 1.740746 object centre at (A) : 9.849500 -34.49250 26.21550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4333606 1.5829757E-02 midg,1,midg; midg,igrid,midg 0.4126051 0.4009998 1,midg,midg; igrid,midg,midg 0.1787084 2.6913047E-02 gauss-seidel spectral radius is 0.9992239 estimated iterations to convergence 283 setup time was (sec) 1.670000 now iterating at: 09:54:26 rms-change max change #iterations 9.341765 352.4862 at 10iterations 5.526810 146.7838 at 20iterations 3.212081 84.68430 at 30iterations 1.859476 46.58777 at 40iterations 1.071926 25.41807 at 50iterations 0.6148115 16.19656 at 60iterations 0.3519130 8.183880 at 70iterations 0.2014938 5.653927 at 80iterations 0.1145924 2.557982 at 90iterations 6.5358050E-02 1.456856 at 100iterations 3.7286680E-02 0.7970810 at 110iterations 2.1191303E-02 0.4766922 at 120iterations 1.2032239E-02 0.3107713 at 130iterations 6.8532373E-03 0.1387444 at 140iterations 3.8793457E-03 8.6425781E-02 at 150iterations 2.2080070E-03 5.0373077E-02 at 160iterations 1.2496982E-03 2.8305054E-02 at 170iterations 7.0864410E-04 1.4777064E-02 at 180iterations finished qdiffx linear iterations at : 09:54:40 total time elapsed so far: 15.41000 # loops : 180 mean,max change (kT/e) : 7.0864410E-04 1.4777064E-02 energy calculations done at 15.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.59000 DelPhi exited at 09:54:41 15.591u 0.257s 0:16.16 98.0% 0+0k 0+0io 0pf+0w