Sun Oct 9 17:13:14 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 Sun Oct 9 2011 at 17:13:14 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3258 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5718876 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): -11.12100 51.12900 ymin,ymax (A): -12.43600 40.32700 zmin,zma (A): 20.22800 76.06800 x,y,z range (A): 62.25000 52.76300 55.84000 scale (grids/A): 0.5718876 object centre (A): 20.00400 13.94550 48.14800 number of atom coordinates read : 3258 total number of charged atoms : 3129 net assigned charge : 4.621025 assigned positive charge : 506.9989 centred at (gu) : 91.06746 89.86135 88.03244 assigned negative charge : -502.3791 centred at (gu) : 90.91797 89.96557 87.96602 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7130 nv = 96 ne = 84 npr = 62735 no. pairs analyzed = 62735 no. exposed pairs = 4429 no. arc points = 31361 no. surface atoms = 1483 nbur = 1775 mkacc time = 0.1800000 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= 336 mr = 3520 m= 3 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 3934 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3033 ## 312 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8923 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.5758300E-10 1.2551977E-09 midg,1,midg; midg,igrid,midg 2.7772595E-09 -1.1968779E-09 1,midg,midg; igrid,midg,midg -1.6316762E-09 4.5416866E-09 gauss-seidel spectral radius is 0.9842501 estimated iterations to convergence 65 setup time was (sec) 0.6900000 now iterating at: 17:13:15 rms-change max change #iterations 9.6417598E-02 15.17603 at 10iterations 7.3059960E-03 1.213989 at 20iterations 6.9209293E-04 0.1136169 at 30iterations 2.1390952E-04 3.0569792E-02 at 40iterations 1.0948558E-04 1.6055107E-02 at 50iterations finished qdiffx linear iterations at : 17:13:18 total time elapsed so far: 3.970000 # loops : 50 mean,max change (kT/e) : 1.0948558E-04 1.6055107E-02 energy calculations done at 3.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.140000 DelPhi exited at 17:13:19 4.141u 0.241s 0:04.67 93.7% 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 Sun Oct 9 2011 at 17:13:19 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 = 3258 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.715663 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): -11.12100 51.12900 ymin,ymax (A): -12.43600 40.32700 zmin,zma (A): 20.22800 76.06800 x,y,z range (A): 62.25000 52.76300 55.84000 scale (grids/A): 1.715663 object centre (A): 20.00400 13.94550 48.14800 number of atom coordinates read : 3258 total number of charged atoms : 3129 net assigned charge : 4.621025 assigned positive charge : 506.9989 centred at (gu) : 93.20119 89.58311 84.09641 assigned negative charge : -502.3791 centred at (gu) : 92.75349 89.89623 83.89765 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 77618 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31361 grid for indexing accessible points = 1.400000 m= 26137 mr = 51356 m= 3281 mr = 17662 m= 110 mr = 1562 m= 0 mr = 6 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7000000 number of dielectric boundary points 36560 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 265 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 24226 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) : 0.5718876 object centre at (A) : 20.00400 13.94550 48.14800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7751175E-03 7.7118669E-03 midg,1,midg; midg,igrid,midg 1.7952692E-02 -8.9765666E-03 1,midg,midg; igrid,midg,midg -5.7004304E-03 2.4236273E-02 gauss-seidel spectral radius is 0.9983962 estimated iterations to convergence 198 setup time was (sec) 1.000000 now iterating at: 17:13:20 rms-change max change #iterations 3.997718 164.8548 at 10iterations 1.755620 66.90913 at 20iterations 0.7733443 24.79708 at 30iterations 0.3404482 11.18483 at 40iterations 0.1505641 5.352297 at 50iterations 6.6250309E-02 2.132630 at 60iterations 2.9277474E-02 0.9482193 at 70iterations 1.2869215E-02 0.4190636 at 80iterations 5.6833653E-03 0.1884117 at 90iterations 2.4986656E-03 7.6839447E-02 at 100iterations 1.1046201E-03 4.0760517E-02 at 110iterations 4.8587867E-04 1.7278314E-02 at 120iterations finished qdiffx linear iterations at : 17:13:28 total time elapsed so far: 9.340000 # loops : 120 mean,max change (kT/e) : 4.8587867E-04 1.7278314E-02 energy calculations done at 9.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.510000 DelPhi exited at 17:13:29 9.516u 0.280s 0:10.05 97.4% 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 17:13:29 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3258 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.573494 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): -11.12100 51.12900 ymin,ymax (A): -12.43600 40.32700 zmin,zma (A): 20.22800 76.06800 x,y,z range (A): 62.25000 52.76300 55.84000 scale (grids/A): 2.573494 object centre (A): 20.00400 13.94550 48.14800 number of atom coordinates read : 3258 total number of charged atoms : 3129 net assigned charge : 4.621025 assigned positive charge : 506.9989 centred at (gu) : 94.80165 89.37427 81.14454 assigned negative charge : -502.3791 centred at (gu) : 94.13009 89.84425 80.84657 start vw surface at 0.1800000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 179747 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31361 grid for indexing accessible points = 1.400000 m= 86506 mr = 126254 m= 28284 mr = 67321 m= 5275 mr = 20903 m= 485 mr = 3283 m= 13 mr = 222 m= 0 mr = 0 time to grow re-entrant surface = 1.080000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.760000 number of dielectric boundary points 82327 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 25021 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) : 1.715663 object centre at (A) : 20.00400 13.94550 48.14800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1384646 7.9748586E-02 midg,1,midg; midg,igrid,midg 0.2685458 -0.1922788 1,midg,midg; igrid,midg,midg 0.1303438 0.2716711 gauss-seidel spectral radius is 0.9992189 estimated iterations to convergence 282 setup time was (sec) 2.080000 now iterating at: 17:13:31 rms-change max change #iterations 10.30667 296.9456 at 10iterations 6.083088 185.7217 at 20iterations 3.543952 82.75366 at 30iterations 2.049618 45.99038 at 40iterations 1.183958 25.26485 at 50iterations 0.6782512 13.62807 at 60iterations 0.3878778 8.614421 at 70iterations 0.2220742 4.908726 at 80iterations 0.1264804 2.602964 at 90iterations 7.2115518E-02 1.438766 at 100iterations 4.0986519E-02 0.8586082 at 110iterations 2.3366716E-02 0.4619751 at 120iterations 1.3281014E-02 0.2802067 at 130iterations 7.5700278E-03 0.1579137 at 140iterations 4.3265144E-03 8.2085609E-02 at 150iterations 2.4932267E-03 4.6216726E-02 at 160iterations 1.4631989E-03 3.0653954E-02 at 170iterations 8.9408219E-04 1.8184185E-02 at 180iterations finished qdiffx linear iterations at : 17:13:45 total time elapsed so far: 15.86000 # loops : 180 mean,max change (kT/e) : 8.9408219E-04 1.8184185E-02 energy calculations done at 15.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.04000 DelPhi exited at 17:13:45 16.046u 0.304s 0:16.61 98.3% 0+0k 0+0io 0pf+0w