Mon Oct 10 14:00:12 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 Mon Oct 10 2011 at 14:00:12 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4452 !!! WARNING: HEM 915 has a net charge of 1.4000 !!! WARNING: FE 3 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: 0.5097146 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): 2.988000 61.92700 ymin,ymax (A): -50.09100 16.64900 zmin,zma (A): -16.17900 53.66400 x,y,z range (A): 58.93900 66.74000 69.84300 scale (grids/A): 0.5097146 object centre (A): 32.45750 -16.72100 18.74250 number of atom coordinates read : 4452 total number of charged atoms : 4220 net assigned charge : 7.300029 assigned positive charge : 647.1337 centred at (gu) : 90.03148 88.57873 93.91859 assigned negative charge : -639.8376 centred at (gu) : 89.96813 88.45641 93.96348 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7444 nv = 96 ne = 84 npr = 89287 no. pairs analyzed = 89287 no. exposed pairs = 5834 no. arc points = 41572 no. surface atoms = 1969 nbur = 2483 mkacc time = 0.2500000 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 = 1.680000 m= 280 mr = 3614 m= 0 mr = 4 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 4106 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3983 ## 565 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 9842 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.4447580E-11 8.5600667E-12 midg,1,midg; midg,igrid,midg -2.4496205E-10 2.5367658E-10 1,midg,midg; igrid,midg,midg -3.3014966E-11 2.4490576E-10 gauss-seidel spectral radius is 0.9803085 estimated iterations to convergence 59 setup time was (sec) 0.7800000 now iterating at: 14:00:13 rms-change max change #iterations 6.3931026E-02 10.67629 at 10iterations 4.2522470E-03 0.6312561 at 20iterations 6.1349524E-04 7.3246002E-02 at 30iterations 1.3773169E-04 1.4017105E-02 at 40iterations 3.2410793E-05 3.3903122E-03 at 50iterations finished qdiffx linear iterations at : 14:00:17 total time elapsed so far: 4.090000 # loops : 50 mean,max change (kT/e) : 3.2410793E-05 3.3903122E-03 energy calculations done at 4.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.250000 DelPhi exited at 14:00:18 4.258u 0.269s 0:05.38 83.8% 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 14:00:18 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4452 !!! WARNING: HEM 915 has a net charge of 1.4000 !!! WARNING: FE 3 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: 1.529144 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): 2.988000 61.92700 ymin,ymax (A): -50.09100 16.64900 zmin,zma (A): -16.17900 53.66400 x,y,z range (A): 58.93900 66.74000 69.84300 scale (grids/A): 1.529144 object centre (A): 32.45750 -16.72100 18.74250 number of atom coordinates read : 4452 total number of charged atoms : 4220 net assigned charge : 7.300029 assigned positive charge : 647.1337 centred at (gu) : 90.09303 85.73492 101.7541 assigned negative charge : -639.8376 centred at (gu) : 89.90384 85.36870 101.8900 start vw surface at 0.2100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 83608 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41572 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 23929 mr = 54853 m= 2283 mr = 15835 m= 45 mr = 986 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7600000 number of dielectric boundary points 38191 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 451 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 31721 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) : 0.5097146 object centre at (A) : 32.45750 -16.72100 18.74250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7756602E-02 2.6371870E-02 midg,1,midg; midg,igrid,midg -1.8703774E-02 7.9823863E-03 1,midg,midg; igrid,midg,midg -9.4042774E-03 1.1202908E-02 gauss-seidel spectral radius is 0.9980820 estimated iterations to convergence 181 setup time was (sec) 1.060000 now iterating at: 14:00:19 rms-change max change #iterations 3.575864 154.3055 at 10iterations 1.448515 55.04903 at 20iterations 0.5870537 18.90581 at 30iterations 0.2390036 8.067138 at 40iterations 9.7592019E-02 3.645260 at 50iterations 3.9728384E-02 1.424253 at 60iterations 1.6236553E-02 0.5719872 at 70iterations 6.7258766E-03 0.2259419 at 80iterations 2.7770936E-03 9.2857361E-02 at 90iterations 1.1599730E-03 3.7807465E-02 at 100iterations 5.0451665E-04 1.6160965E-02 at 110iterations 2.2968734E-04 7.7304840E-03 at 120iterations finished qdiffx linear iterations at : 14:00:28 total time elapsed so far: 9.460000 # loops : 120 mean,max change (kT/e) : 2.2968734E-04 7.7304840E-03 energy calculations done at 9.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.650000 DelPhi exited at 14:00:30 9.650u 0.279s 0:12.35 80.3% 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 14:00:30 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4452 !!! WARNING: HEM 915 has a net charge of 1.4000 !!! WARNING: FE 3 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: 2.293716 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): 2.988000 61.92700 ymin,ymax (A): -50.09100 16.64900 zmin,zma (A): -16.17900 53.66400 x,y,z range (A): 58.93900 66.74000 69.84300 scale (grids/A): 2.293716 object centre (A): 32.45750 -16.72100 18.74250 number of atom coordinates read : 4452 total number of charged atoms : 4220 net assigned charge : 7.300029 assigned positive charge : 647.1337 centred at (gu) : 90.13901 83.60185 107.6309 assigned negative charge : -639.8376 centred at (gu) : 89.85570 83.05301 107.8347 start vw surface at 0.2100000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 194680 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41572 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 84428 mr = 135643 m= 22722 mr = 64970 m= 3247 mr = 16335 m= 158 mr = 1985 m= 3 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.820000 number of dielectric boundary points 86249 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 73 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 33672 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) : 1.529144 object centre at (A) : 32.45750 -16.72100 18.74250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3978697 0.6462056 midg,1,midg; midg,igrid,midg -0.3273316 5.4913793E-02 1,midg,midg; igrid,midg,midg -0.1618897 0.1976222 gauss-seidel spectral radius is 0.9991474 estimated iterations to convergence 271 setup time was (sec) 2.150000 now iterating at: 14:00:33 rms-change max change #iterations 9.721887 260.1599 at 10iterations 5.565156 121.6263 at 20iterations 3.151760 69.05348 at 30iterations 1.771048 35.66915 at 40iterations 0.9939212 20.75773 at 50iterations 0.5550417 11.06784 at 60iterations 0.3093680 6.410870 at 70iterations 0.1716282 3.290129 at 80iterations 9.5435858E-02 2.203388 at 90iterations 5.3006522E-02 1.020041 at 100iterations 2.9280638E-02 0.6329532 at 110iterations 1.6237535E-02 0.3144512 at 120iterations 8.9982636E-03 0.1871643 at 130iterations 4.9797189E-03 9.8217010E-02 at 140iterations 2.7506945E-03 5.1025391E-02 at 150iterations 1.5281627E-03 2.8405190E-02 at 160iterations 8.4941869E-04 1.7150879E-02 at 170iterations 4.7209967E-04 9.2287064E-03 at 180iterations finished qdiffx linear iterations at : 14:00:47 total time elapsed so far: 16.15000 # loops : 180 mean,max change (kT/e) : 4.7209967E-04 9.2287064E-03 energy calculations done at 16.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.33000 DelPhi exited at 14:00:47 16.334u 0.325s 0:17.20 96.8% 0+0k 0+0io 0pf+0w