Sun Oct 9 03:47:17 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 Sun Oct 9 2011 at 03:47:17 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 # of charge parameter records: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4744 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 has a net charge of 1.4000 !!! WARNING: FE 5 has a net charge of 1.4000 !!! WARNING: FE 6 has a net charge of 1.4000 !!! WARNING: FE 7 has a net charge of 1.4000 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: 0.4094778 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): -2.673000 79.27200 ymin,ymax (A): -12.57700 55.66600 zmin,zma (A): -16.11500 70.82500 x,y,z range (A): 81.94500 68.24300 86.94000 scale (grids/A): 0.4094778 object centre (A): 38.29950 21.54450 27.35500 number of atom coordinates read : 4744 total number of charged atoms : 4425 net assigned charge : 21.30000 assigned positive charge : 691.9059 centred at (gu) : 85.73528 91.67384 83.53478 assigned negative charge : -670.6109 centred at (gu) : 85.56059 91.74247 83.44153 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 4576 nv = 96 ne = 84 npr = 96221 no. pairs analyzed = 96221 no. exposed pairs = 6189 no. arc points = 43014 no. surface atoms = 2081 nbur = 2663 mkacc time = 0.2000000 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 = 2.044000 m= 104 mr = 2012 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 2668 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3104 ## 719 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 6163 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3743558E-12 2.8016630E-13 midg,1,midg; midg,igrid,midg 1.0797682E-12 8.0043893E-13 1,midg,midg; igrid,midg,midg -2.7702244E-12 7.4315966E-13 gauss-seidel spectral radius is 0.9696528 estimated iterations to convergence 48 setup time was (sec) 0.6700000 now iterating at: 03:47:18 rms-change max change #iterations 2.1629937E-02 4.283882 at 10iterations 2.5191805E-03 0.4420004 at 20iterations 7.2397455E-04 0.1325932 at 30iterations 2.1366666E-04 4.0184021E-02 at 40iterations 6.3317340E-05 1.2029648E-02 at 50iterations finished qdiffx linear iterations at : 03:47:21 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 6.3317340E-05 1.2029648E-02 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 03:47:21 3.528u 0.195s 0:04.08 90.9% 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 Sun Oct 9 2011 at 03:47:21 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4744 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 has a net charge of 1.4000 !!! WARNING: FE 5 has a net charge of 1.4000 !!! WARNING: FE 6 has a net charge of 1.4000 !!! WARNING: FE 7 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 1.228433 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): -2.673000 79.27200 ymin,ymax (A): -12.57700 55.66600 zmin,zma (A): -16.11500 70.82500 x,y,z range (A): 81.94500 68.24300 86.94000 scale (grids/A): 1.228433 object centre (A): 38.29950 21.54450 27.35500 number of atom coordinates read : 4744 total number of charged atoms : 4425 net assigned charge : 21.30000 assigned positive charge : 691.9059 centred at (gu) : 77.20419 95.02011 70.60252 assigned negative charge : -670.6109 centred at (gu) : 76.68140 95.22741 70.32426 start vw surface at 0.2400000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 53682 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43014 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.904000 m= 11088 mr = 33472 m= 415 mr = 6309 m= 4 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 74 time to turn everything in is 0.5000000 number of dielectric boundary points 25355 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 796 ## 37 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 29818 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) : 0.4094778 object centre at (A) : 38.29950 21.54450 27.35500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2030471E-02 1.4267674E-03 midg,1,midg; midg,igrid,midg 1.9639828E-03 1.0547525E-03 1,midg,midg; igrid,midg,midg -8.1906345E-04 1.2198999E-03 gauss-seidel spectral radius is 0.9968063 estimated iterations to convergence 141 setup time was (sec) 0.7700000 now iterating at: 03:47:22 rms-change max change #iterations 2.080508 111.0762 at 10iterations 0.6473294 29.07873 at 20iterations 0.2036494 8.519733 at 30iterations 6.5014325E-02 3.290852 at 40iterations 2.1008087E-02 0.9211006 at 50iterations 7.5624795E-03 0.3488417 at 60iterations 3.4139121E-03 0.1626091 at 70iterations 1.9476571E-03 8.3868027E-02 at 80iterations 1.2547295E-03 5.2917480E-02 at 90iterations 8.3607819E-04 3.5121918E-02 at 100iterations 5.6197046E-04 2.3788452E-02 at 110iterations 3.7861156E-04 1.6094208E-02 at 120iterations finished qdiffx linear iterations at : 03:47:28 total time elapsed so far: 6.780000 # loops : 120 mean,max change (kT/e) : 3.7861156E-04 1.6094208E-02 energy calculations done at 6.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.980000 DelPhi exited at 03:47:29 6.984u 0.189s 0:07.45 96.1% 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 Sun Oct 9 2011 at 03:47:29 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 # of charge parameter records: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4744 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 has a net charge of 1.4000 !!! WARNING: FE 5 has a net charge of 1.4000 !!! WARNING: FE 6 has a net charge of 1.4000 !!! WARNING: FE 7 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.842650 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): -2.673000 79.27200 ymin,ymax (A): -12.57700 55.66600 zmin,zma (A): -16.11500 70.82500 x,y,z range (A): 81.94500 68.24300 86.94000 scale (grids/A): 1.842650 object centre (A): 38.29950 21.54450 27.35500 number of atom coordinates read : 4744 total number of charged atoms : 4425 net assigned charge : 21.30000 assigned positive charge : 691.9059 centred at (gu) : 70.80585 97.52988 60.90339 assigned negative charge : -670.6109 centred at (gu) : 70.02200 97.84107 60.48635 start vw surface at 0.1900000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 126007 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43014 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.876000 m= 44046 mr = 84290 m= 6807 mr = 31355 m= 309 mr = 4109 m= 1 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 256 time to turn everything in is 0.9600000 number of dielectric boundary points 57351 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 269 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 34713 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) : 1.228433 object centre at (A) : 38.29950 21.54450 27.35500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4347157 2.1576826E-02 midg,1,midg; midg,igrid,midg 4.8962828E-02 2.1271568E-02 1,midg,midg; igrid,midg,midg 4.4212237E-04 1.7452210E-02 gauss-seidel spectral radius is 0.9986199 estimated iterations to convergence 213 setup time was (sec) 1.270000 now iterating at: 03:47:30 rms-change max change #iterations 6.502498 254.3760 at 10iterations 3.161414 98.65952 at 20iterations 1.522845 49.74647 at 30iterations 0.7304364 20.94697 at 40iterations 0.3472248 9.333506 at 50iterations 0.1641911 4.312096 at 60iterations 7.8026690E-02 2.184435 at 70iterations 3.6951616E-02 0.9773500 at 80iterations 1.7464560E-02 0.4532013 at 90iterations 8.2927672E-03 0.2190512 at 100iterations 3.9601810E-03 9.6988678E-02 at 110iterations 1.9252166E-03 5.3956985E-02 at 120iterations 9.7834191E-04 2.7938843E-02 at 130iterations 5.3859159E-04 1.4999390E-02 at 140iterations 3.2636608E-04 8.9683533E-03 at 150iterations 2.1827106E-04 5.6743622E-03 at 160iterations 1.5551074E-04 3.8280487E-03 at 170iterations 1.1482917E-04 2.6359558E-03 at 180iterations finished qdiffx linear iterations at : 03:47:40 total time elapsed so far: 11.47000 # loops : 180 mean,max change (kT/e) : 1.1482917E-04 2.6359558E-03 energy calculations done at 11.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.64000 DelPhi exited at 03:47:41 11.647u 0.243s 0:12.21 97.2% 0+0k 0+0io 0pf+0w