Tue Oct 11 00:36:20 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 Tue Oct 11 2011 at 00:36:20 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2637 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6238062 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): 13.26600 70.33500 ymin,ymax (A): -11.41500 44.31200 zmin,zma (A): 34.58500 77.14000 x,y,z range (A): 57.06900 55.72700 42.55500 scale (grids/A): 0.6238062 object centre (A): 41.80050 16.44850 55.86250 number of atom coordinates read : 2637 total number of charged atoms : 2493 net assigned charge : 3.500015 assigned positive charge : 395.9777 centred at (gu) : 91.47699 89.73046 90.14505 assigned negative charge : -392.4784 centred at (gu) : 91.21870 89.90566 89.93504 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6786 nv = 96 ne = 84 npr = 53981 no. pairs analyzed = 53981 no. exposed pairs = 3049 no. arc points = 21473 no. surface atoms = 1030 nbur = 1607 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 345 mr = 3898 m= 0 mr = 33 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 115 time to turn everything in is 0.3500000 number of dielectric boundary points 3200 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2096 ## 213 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8298 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2856147E-08 1.8797872E-08 midg,1,midg; midg,igrid,midg 1.6670166E-08 -9.9357083E-09 1,midg,midg; igrid,midg,midg -1.2282590E-08 3.0097222E-08 gauss-seidel spectral radius is 0.9866906 estimated iterations to convergence 71 setup time was (sec) 0.6300000 now iterating at: 00:36:21 rms-change max change #iterations 0.1318837 19.65047 at 10iterations 1.2834147E-02 1.970173 at 20iterations 1.4412301E-03 0.3064194 at 30iterations 2.3717117E-04 5.1589966E-02 at 40iterations 4.7676971E-05 1.1466980E-02 at 50iterations finished qdiffx linear iterations at : 00:36:24 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 4.7676971E-05 1.1466980E-02 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.140000 DelPhi exited at 00:36:25 4.145u 0.266s 0:04.93 89.2% 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 Tue Oct 11 2011 at 00:36:25 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2637 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.871419 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): 13.26600 70.33500 ymin,ymax (A): -11.41500 44.31200 zmin,zma (A): 34.58500 77.14000 x,y,z range (A): 57.06900 55.72700 42.55500 scale (grids/A): 1.871419 object centre (A): 41.80050 16.44850 55.86250 number of atom coordinates read : 2637 total number of charged atoms : 2493 net assigned charge : 3.500015 assigned positive charge : 395.9777 centred at (gu) : 94.43038 89.19067 90.43436 assigned negative charge : -392.4784 centred at (gu) : 93.65587 89.71677 89.80499 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 74171 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21473 grid for indexing accessible points = 1.400000 m= 26427 mr = 52808 m= 3718 mr = 19773 m= 140 mr = 2366 m= 4 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 3883 time to turn everything in is 0.6400000 number of dielectric boundary points 29476 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 161 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 19595 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) : 0.6238062 object centre at (A) : 41.80050 16.44850 55.86250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.4947865E-04 3.2921892E-02 midg,1,midg; midg,igrid,midg 4.2495813E-02 -2.7688235E-02 1,midg,midg; igrid,midg,midg -6.0085744E-02 -1.3956211E-02 gauss-seidel spectral radius is 0.9985873 estimated iterations to convergence 211 setup time was (sec) 0.9200000 now iterating at: 00:36:26 rms-change max change #iterations 4.113719 172.9847 at 10iterations 1.895072 66.09110 at 20iterations 0.8742349 30.89667 at 30iterations 0.4062048 13.04355 at 40iterations 0.1880697 6.084778 at 50iterations 8.7066203E-02 2.697968 at 60iterations 4.0389072E-02 1.397076 at 70iterations 1.8749561E-02 0.5975418 at 80iterations 8.7547842E-03 0.2668686 at 90iterations 4.1260612E-03 0.1357193 at 100iterations 1.9730669E-03 7.3062897E-02 at 110iterations 9.7566098E-04 3.7132263E-02 at 120iterations finished qdiffx linear iterations at : 00:36:34 total time elapsed so far: 9.320000 # loops : 120 mean,max change (kT/e) : 9.7566098E-04 3.7132263E-02 energy calculations done at 9.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.500000 DelPhi exited at 00:36:35 9.501u 0.346s 0:10.23 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 Tue Oct 11 2011 at 00:36:35 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2637 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.807128 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): 13.26600 70.33500 ymin,ymax (A): -11.41500 44.31200 zmin,zma (A): 34.58500 77.14000 x,y,z range (A): 57.06900 55.72700 42.55500 scale (grids/A): 2.807128 object centre (A): 41.80050 16.44850 55.86250 number of atom coordinates read : 2637 total number of charged atoms : 2493 net assigned charge : 3.500015 assigned positive charge : 395.9777 centred at (gu) : 96.64552 88.78575 90.65150 assigned negative charge : -392.4784 centred at (gu) : 95.48376 89.57498 89.70734 start vw surface at 0.1600000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 172072 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21473 grid for indexing accessible points = 1.400000 m= 86684 mr = 127769 m= 30123 mr = 71929 m= 6453 mr = 24526 m= 711 mr = 4889 m= 27 mr = 453 m= 0 mr = 2 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 13126 time to turn everything in is 1.640000 number of dielectric boundary points 66502 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 19940 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) : 1.871419 object centre at (A) : 41.80050 16.44850 55.86250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0485436E-02 0.3173158 midg,1,midg; midg,igrid,midg 0.5623409 -0.4195355 1,midg,midg; igrid,midg,midg -0.7416892 -0.2146698 gauss-seidel spectral radius is 0.9992410 estimated iterations to convergence 287 setup time was (sec) 1.970000 now iterating at: 00:36:37 rms-change max change #iterations 9.628345 323.2939 at 10iterations 5.529931 126.6876 at 20iterations 3.170650 63.20740 at 30iterations 1.813388 33.83452 at 40iterations 1.035298 18.81468 at 50iterations 0.5900511 11.34261 at 60iterations 0.3370399 6.185902 at 70iterations 0.1919653 4.012669 at 80iterations 0.1093657 2.079651 at 90iterations 6.2631011E-02 1.174423 at 100iterations 3.5786875E-02 0.6197472 at 110iterations 2.0489851E-02 0.3892441 at 120iterations 1.1767618E-02 0.2237091 at 130iterations 6.8115224E-03 0.1255159 at 140iterations 3.9823744E-03 8.1592560E-02 at 150iterations 2.3815595E-03 5.0064087E-02 at 160iterations 1.4621885E-03 3.3370972E-02 at 170iterations 9.4058568E-04 2.3239136E-02 at 180iterations finished qdiffx linear iterations at : 00:36:51 total time elapsed so far: 15.68000 # loops : 180 mean,max change (kT/e) : 9.4058568E-04 2.3239136E-02 energy calculations done at 15.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.88000 DelPhi exited at 00:36:52 15.877u 0.328s 0:16.75 96.6% 0+0k 0+0io 0pf+0w