Mon Oct 10 14:04:04 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 14:04:04 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: 373 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4618 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: FAD 994 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5467671 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): 16.93800 78.87900 ymin,ymax (A): 118.5760 183.6860 zmin,zma (A): -1.789000 59.49800 x,y,z range (A): 61.94100 65.10999 61.28700 scale (grids/A): 0.5467671 object centre (A): 47.90850 151.1310 28.85450 number of atom coordinates read : 4618 total number of charged atoms : 4443 net assigned charge : 1.906037 assigned positive charge : 708.8004 centred at (gu) : 91.60926 89.28324 87.36050 assigned negative charge : -706.8979 centred at (gu) : 91.54710 89.20296 87.37895 start vw surface at 0.2100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8822 nv = 96 ne = 84 npr = 93321 no. pairs analyzed = 93321 no. exposed pairs = 5489 no. arc points = 38465 no. surface atoms = 1850 nbur = 2768 mkacc time = 0.2600000 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 = 1.568000 m= 403 mr = 4788 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.5400000 number of dielectric boundary points 4403 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3960 ## 519 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 11801 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.9731725E-10 -4.4135747E-11 midg,1,midg; midg,igrid,midg -9.1315083E-10 8.0657359E-10 1,midg,midg; igrid,midg,midg -3.7544665E-10 1.1593463E-09 gauss-seidel spectral radius is 0.9828745 estimated iterations to convergence 63 setup time was (sec) 0.8100000 now iterating at: 14:04:05 rms-change max change #iterations 9.4903871E-02 14.23357 at 10iterations 6.6356864E-03 0.9412766 at 20iterations 5.6129351E-04 8.4795952E-02 at 30iterations 1.0837759E-04 1.6959667E-02 at 40iterations 3.3718610E-05 5.2976608E-03 at 50iterations finished qdiffx linear iterations at : 14:04:09 total time elapsed so far: 4.110000 # loops : 50 mean,max change (kT/e) : 3.3718610E-05 5.2976608E-03 energy calculations done at 4.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.290000 DelPhi exited at 14:04:09 4.291u 0.243s 0:05.05 89.7% 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 14:04:09 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 # of charge parameter records: 373 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4618 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: FAD 994 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.640301 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): 16.93800 78.87900 ymin,ymax (A): 118.5760 183.6860 zmin,zma (A): -1.789000 59.49800 x,y,z range (A): 61.94100 65.10999 61.28700 scale (grids/A): 1.640301 object centre (A): 47.90850 151.1310 28.85450 number of atom coordinates read : 4618 total number of charged atoms : 4443 net assigned charge : 1.906037 assigned positive charge : 708.8004 centred at (gu) : 94.82633 87.84845 82.08041 assigned negative charge : -706.8979 centred at (gu) : 94.64103 87.60829 82.13667 start vw surface at 0.2300000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 99227 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38465 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30925 mr = 69653 m= 3596 mr = 21496 m= 123 mr = 1982 m= 0 mr = 19 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 1040 time to turn everything in is 0.8700000 number of dielectric boundary points 40721 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 474 ## 3 charges are in solution ## iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 34051 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) : 0.5467671 object centre at (A) : 47.90850 151.1310 28.85450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5462945E-03 8.1767989E-03 midg,1,midg; midg,igrid,midg 1.3287080E-02 3.0160103E-02 1,midg,midg; igrid,midg,midg -2.0113815E-02 -1.4004175E-02 gauss-seidel spectral radius is 0.9983553 estimated iterations to convergence 196 setup time was (sec) 1.180000 now iterating at: 14:04:11 rms-change max change #iterations 4.390689 211.8905 at 10iterations 1.906222 74.82179 at 20iterations 0.8268564 34.37192 at 30iterations 0.3594262 11.21923 at 40iterations 0.1568580 5.266087 at 50iterations 6.8353467E-02 2.136520 at 60iterations 2.9843425E-02 0.9434929 at 70iterations 1.3003502E-02 0.3834639 at 80iterations 5.6512551E-03 0.1657327 at 90iterations 2.4747618E-03 7.5483322E-02 at 100iterations 1.0811321E-03 3.6453247E-02 at 110iterations 4.7427538E-04 1.3525963E-02 at 120iterations finished qdiffx linear iterations at : 14:04:19 total time elapsed so far: 9.680000 # loops : 120 mean,max change (kT/e) : 4.7427538E-04 1.3525963E-02 energy calculations done at 9.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.860000 DelPhi exited at 14:04:20 9.860u 0.273s 0:10.67 94.9% 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 14:04:20 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: 373 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4618 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: FAD 994 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.460452 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): 16.93800 78.87900 ymin,ymax (A): 118.5760 183.6860 zmin,zma (A): -1.789000 59.49800 x,y,z range (A): 61.94100 65.10999 61.28700 scale (grids/A): 2.460452 object centre (A): 47.90850 151.1310 28.85450 number of atom coordinates read : 4618 total number of charged atoms : 4443 net assigned charge : 1.906037 assigned positive charge : 708.8004 centred at (gu) : 97.23923 86.77235 78.12040 assigned negative charge : -706.8979 centred at (gu) : 96.96136 86.41247 78.20488 start vw surface at 0.2100000 fill in re-entrant regions at 0.7100000 boundary points on vw surface= 231172 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38465 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 107270 mr = 170393 m= 31557 mr = 85737 m= 5953 mr = 23858 m= 529 mr = 4258 m= 6 mr = 300 m= 0 mr = 0 time to grow re-entrant surface = 1.300000 no. cavity mid-points inaccessible to solvent = 3440 time to turn everything in is 2.140000 number of dielectric boundary points 91941 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 29 iepsmp to db, and charging done at 2.310000 number of grid points assigned charge 35502 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) : 1.640301 object centre at (A) : 47.90850 151.1310 28.85450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0735292E-03 0.1733544 midg,1,midg; midg,igrid,midg 0.2133330 0.5491311 1,midg,midg; igrid,midg,midg -0.3655911 -0.2597600 gauss-seidel spectral radius is 0.9992193 estimated iterations to convergence 283 setup time was (sec) 2.480000 now iterating at: 14:04:23 rms-change max change #iterations 11.19742 369.3960 at 10iterations 6.469430 164.0080 at 20iterations 3.714059 85.57543 at 30iterations 2.130869 41.18343 at 40iterations 1.217661 21.57993 at 50iterations 0.6925649 12.35180 at 60iterations 0.3939378 6.731276 at 70iterations 0.2236436 4.808490 at 80iterations 0.1270610 2.333382 at 90iterations 7.2020844E-02 1.206959 at 100iterations 4.0853765E-02 0.6836166 at 110iterations 2.3217818E-02 0.4064579 at 120iterations 1.3140898E-02 0.2220860 at 130iterations 7.4542747E-03 0.1323853 at 140iterations 4.2343717E-03 6.7388058E-02 at 150iterations 2.4060498E-03 4.3090820E-02 at 160iterations 1.3670096E-03 2.3220062E-02 at 170iterations 7.8654720E-04 1.3303757E-02 at 180iterations finished qdiffx linear iterations at : 14:04:37 total time elapsed so far: 16.74000 # loops : 180 mean,max change (kT/e) : 7.8654720E-04 1.3303757E-02 energy calculations done at 16.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.92000 DelPhi exited at 14:04:38 16.917u 0.301s 0:17.66 97.4% 0+0k 0+0io 0pf+0w