Tue Oct 11 06:38:15 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 Tue Oct 11 2011 at 06:38:15 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2045 !!! WARNING: HIR 58 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7069664 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): -21.07000 24.50000 ymin,ymax (A): -26.78400 10.66700 zmin,zma (A): -14.05700 36.29900 x,y,z range (A): 45.57000 37.45100 50.35600 scale (grids/A): 0.7069664 object centre (A): 1.715000 -8.058500 11.12100 number of atom coordinates read : 2045 total number of charged atoms : 1931 net assigned charge : 6.945010 assigned positive charge : 314.4191 centred at (gu) : 90.05096 90.87405 89.42918 assigned negative charge : -307.4741 centred at (gu) : 89.86287 90.86519 89.40944 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6884 nv = 96 ne = 84 npr = 40871 no. pairs analyzed = 40871 no. exposed pairs = 2481 no. arc points = 17242 no. surface atoms = 847 nbur = 1198 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 442 mr = 3926 m= 7 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3336 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1559 ## 119 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7736 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.3860870E-08 6.0557177E-08 midg,1,midg; midg,igrid,midg 4.5628521E-08 7.3456178E-08 1,midg,midg; igrid,midg,midg -3.4013993E-08 1.4838027E-07 gauss-seidel spectral radius is 0.9895670 estimated iterations to convergence 80 setup time was (sec) 0.5800000 now iterating at: 06:38:16 rms-change max change #iterations 0.1974471 27.86721 at 10iterations 2.4837749E-02 3.941434 at 20iterations 3.2314651E-03 0.5040156 at 30iterations 5.3489400E-04 6.9310188E-02 at 40iterations 1.2704500E-04 1.8377304E-02 at 50iterations finished qdiffx linear iterations at : 06:38:19 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 1.2704500E-04 1.8377304E-02 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.020000 DelPhi exited at 06:38:20 4.025u 0.248s 0:04.56 93.4% 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 Tue Oct 11 2011 at 06:38:20 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2045 !!! WARNING: HIR 58 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.120899 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): -21.07000 24.50000 ymin,ymax (A): -26.78400 10.66700 zmin,zma (A): -14.05700 36.29900 x,y,z range (A): 45.57000 37.45100 50.35600 scale (grids/A): 2.120899 object centre (A): 1.715000 -8.058500 11.12100 number of atom coordinates read : 2045 total number of charged atoms : 1931 net assigned charge : 6.945010 assigned positive charge : 314.4191 centred at (gu) : 90.15294 92.62210 88.28772 assigned negative charge : -307.4741 centred at (gu) : 89.58879 92.59571 88.22838 start vw surface at 0.1300000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 73743 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17242 grid for indexing accessible points = 1.400000 m= 29266 mr = 52322 m= 5692 mr = 22186 m= 538 mr = 3805 m= 10 mr = 277 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 30659 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 79 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 15340 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) : 0.7069664 object centre at (A) : 1.715000 -8.058500 11.12100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9302345E-02 4.4379927E-02 midg,1,midg; midg,igrid,midg 6.8900343E-03 3.3830497E-02 1,midg,midg; igrid,midg,midg 6.3558837E-04 4.1004617E-02 gauss-seidel spectral radius is 0.9988262 estimated iterations to convergence 231 setup time was (sec) 0.9500000 now iterating at: 06:38:21 rms-change max change #iterations 4.587933 188.9682 at 10iterations 2.263395 74.04187 at 20iterations 1.120521 33.70440 at 30iterations 0.5549018 19.55725 at 40iterations 0.2761909 9.477943 at 50iterations 0.1372733 4.339031 at 60iterations 6.8056606E-02 2.062618 at 70iterations 3.3795878E-02 1.027746 at 80iterations 1.6849447E-02 0.4791992 at 90iterations 8.4390687E-03 0.2545366 at 100iterations 4.2364919E-03 0.1299496 at 110iterations 2.1672740E-03 6.4981461E-02 at 120iterations finished qdiffx linear iterations at : 06:38:29 total time elapsed so far: 9.340000 # loops : 120 mean,max change (kT/e) : 2.1672740E-03 6.4981461E-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) 9.530000 DelPhi exited at 06:38:30 9.531u 0.306s 0:10.37 94.7% 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 Tue Oct 11 2011 at 06:38:30 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2045 !!! WARNING: HIR 58 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.181349 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): -21.07000 24.50000 ymin,ymax (A): -26.78400 10.66700 zmin,zma (A): -14.05700 36.29900 x,y,z range (A): 45.57000 37.45100 50.35600 scale (grids/A): 3.181349 object centre (A): 1.715000 -8.058500 11.12100 number of atom coordinates read : 2045 total number of charged atoms : 1931 net assigned charge : 6.945010 assigned positive charge : 314.4191 centred at (gu) : 90.22935 93.93322 87.43173 assigned negative charge : -307.4741 centred at (gu) : 89.38326 93.89361 87.34265 start vw surface at 0.1500000 fill in re-entrant regions at 0.9600000 boundary points on vw surface= 170023 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17242 grid for indexing accessible points = 1.400000 m= 91721 mr = 125880 m= 37113 mr = 76472 m= 10748 mr = 30367 m= 2157 mr = 8333 m= 232 mr = 1578 m= 3 mr = 144 m= 0 mr = 0 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.160000 number of dielectric boundary points 69223 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.300000 number of grid points assigned charge 15448 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) : 2.120899 object centre at (A) : 1.715000 -8.058500 11.12100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5665482 0.4086478 midg,1,midg; midg,igrid,midg 3.9307266E-02 0.2757550 1,midg,midg; igrid,midg,midg 8.0789864E-02 0.3260674 gauss-seidel spectral radius is 0.9992945 estimated iterations to convergence 297 setup time was (sec) 2.470000 now iterating at: 06:38:33 rms-change max change #iterations 10.30634 443.4193 at 10iterations 6.086229 135.5798 at 20iterations 3.590629 71.69597 at 30iterations 2.119430 39.84706 at 40iterations 1.246364 25.32527 at 50iterations 0.7313399 17.30311 at 60iterations 0.4285928 8.874245 at 70iterations 0.2516273 4.583065 at 80iterations 0.1475816 2.592987 at 90iterations 8.6398631E-02 1.464086 at 100iterations 5.0720833E-02 0.9005375 at 110iterations 2.9937984E-02 0.5205090 at 120iterations 1.7722826E-02 0.3368454 at 130iterations 1.0656879E-02 0.2089770 at 140iterations 6.5301522E-03 0.1335258 at 150iterations 4.1413656E-03 7.7560425E-02 at 160iterations 2.7569677E-03 4.9022675E-02 at 170iterations 1.9396014E-03 3.7292480E-02 at 180iterations finished qdiffx linear iterations at : 06:38:46 total time elapsed so far: 16.17000 # loops : 180 mean,max change (kT/e) : 1.9396014E-03 3.7292480E-02 energy calculations done at 16.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.35000 DelPhi exited at 06:38:47 16.350u 0.322s 0:17.27 96.5% 0+0k 0+0io 0pf+0w