Sat Oct 15 13:38:15 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 Sat Oct 15 2011 at 13:38:15 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2853 !!! WARNING: HIT 226 has a net charge of 0.5140 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: 0.5940759 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): -17.16000 35.92300 ymin,ymax (A): -64.45500 -4.530000 zmin,zma (A): -2.768000 57.12400 x,y,z range (A): 53.08300 59.92500 59.89200 scale (grids/A): 0.5940759 object centre (A): 9.381500 -34.49250 27.17800 number of atom coordinates read : 2853 total number of charged atoms : 2699 net assigned charge : 3.014014 assigned positive charge : 419.5438 centred at (gu) : 89.25638 89.36588 87.05161 assigned negative charge : -416.5302 centred at (gu) : 89.39096 89.28503 86.95992 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6780 nv = 96 ne = 84 npr = 55812 no. pairs analyzed = 55812 no. exposed pairs = 4309 no. arc points = 31294 no. surface atoms = 1418 nbur = 1435 mkacc time = 8.9999996E-02 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= 352 mr = 2948 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 4165 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3104 ## 309 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8485 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.7882675E-09 2.0805666E-09 midg,1,midg; midg,igrid,midg -1.7333690E-09 3.2087424E-09 1,midg,midg; igrid,midg,midg 6.4093912E-09 -2.7323963E-09 gauss-seidel spectral radius is 0.9853776 estimated iterations to convergence 68 setup time was (sec) 0.4300000 now iterating at: 13:38:16 rms-change max change #iterations 0.1086050 19.75815 at 10iterations 8.8452632E-03 1.391253 at 20iterations 7.3538790E-04 0.1281872 at 30iterations 6.7768109E-05 9.9544525E-03 at 40iterations 9.2016671E-06 1.2454987E-03 at 50iterations finished qdiffx linear iterations at : 13:38:21 total time elapsed so far: 3.690000 # loops : 50 mean,max change (kT/e) : 9.2016671E-06 1.2454987E-03 energy calculations done at 3.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.820000 DelPhi exited at 13:38:22 3.826u 0.205s 0:07.16 56.1% 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 Sat Oct 15 2011 at 13:38:22 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2853 !!! WARNING: HIT 226 has a net charge of 0.5140 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: 1.782228 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): -17.16000 35.92300 ymin,ymax (A): -64.45500 -4.530000 zmin,zma (A): -2.768000 57.12400 x,y,z range (A): 53.08300 59.92500 59.89200 scale (grids/A): 1.782228 object centre (A): 9.381500 -34.49250 27.17800 number of atom coordinates read : 2853 total number of charged atoms : 2699 net assigned charge : 3.014014 assigned positive charge : 419.5438 centred at (gu) : 87.76875 88.09711 81.15430 assigned negative charge : -416.5302 centred at (gu) : 88.17246 87.85485 80.87955 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 71873 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31294 grid for indexing accessible points = 1.400000 m= 22711 mr = 43683 m= 3151 mr = 14343 m= 154 mr = 1451 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 38382 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 236 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 21022 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) : 0.5940759 object centre at (A) : 9.381500 -34.49250 27.17800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.1768865E-03 4.2051729E-03 midg,1,midg; midg,igrid,midg 1.9795375E-02 3.7554264E-02 1,midg,midg; igrid,midg,midg 1.6213691E-02 -6.8779633E-04 gauss-seidel spectral radius is 0.9984890 estimated iterations to convergence 204 setup time was (sec) 0.6300000 now iterating at: 13:38:23 rms-change max change #iterations 3.897677 165.1137 at 10iterations 1.748994 66.85818 at 20iterations 0.7828412 29.33059 at 30iterations 0.3504250 12.16806 at 40iterations 0.1580215 5.611283 at 50iterations 7.1038917E-02 2.480655 at 60iterations 3.1988896E-02 0.9896164 at 70iterations 1.4367259E-02 0.4496994 at 80iterations 6.4552878E-03 0.2345619 at 90iterations 2.8969646E-03 0.1073532 at 100iterations 1.3013913E-03 4.3502808E-02 at 110iterations 5.8636640E-04 1.8747330E-02 at 120iterations finished qdiffx linear iterations at : 13:38:39 total time elapsed so far: 8.790000 # loops : 120 mean,max change (kT/e) : 5.8636640E-04 1.8747330E-02 energy calculations done at 8.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.930000 DelPhi exited at 13:38:39 8.928u 0.313s 0:17.07 54.0% 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 Sat Oct 15 2011 at 13:38:39 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2853 !!! WARNING: HIT 226 has a net charge of 0.5140 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: 2.673342 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): -17.16000 35.92300 ymin,ymax (A): -64.45500 -4.530000 zmin,zma (A): -2.768000 57.12400 x,y,z range (A): 53.08300 59.92500 59.89200 scale (grids/A): 2.673342 object centre (A): 9.381500 -34.49250 27.17800 number of atom coordinates read : 2853 total number of charged atoms : 2699 net assigned charge : 3.014014 assigned positive charge : 419.5438 centred at (gu) : 86.65313 87.14548 76.73126 assigned negative charge : -416.5302 centred at (gu) : 87.25862 86.78222 76.31921 start vw surface at 0.1000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 165900 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31294 grid for indexing accessible points = 1.400000 m= 74386 mr = 107915 m= 24301 mr = 55118 m= 5162 mr = 17317 m= 642 mr = 3259 m= 17 mr = 314 m= 0 mr = 4 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.000000 number of dielectric boundary points 86481 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 21584 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) : 1.782228 object centre at (A) : 9.381500 -34.49250 27.17800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.7376526E-02 6.4836189E-02 midg,1,midg; midg,igrid,midg 0.7154219 0.4925235 1,midg,midg; igrid,midg,midg 0.1284051 5.7444926E-02 gauss-seidel spectral radius is 0.9992477 estimated iterations to convergence 288 setup time was (sec) 1.300000 now iterating at: 13:38:41 rms-change max change #iterations 9.893083 298.3831 at 10iterations 5.901680 164.2959 at 20iterations 3.471300 101.8406 at 30iterations 2.022987 48.91355 at 40iterations 1.175944 27.02626 at 50iterations 0.6807315 17.37532 at 60iterations 0.3931651 9.173454 at 70iterations 0.2266246 6.122974 at 80iterations 0.1301145 2.938865 at 90iterations 7.4809305E-02 1.468637 at 100iterations 4.2907376E-02 0.8401203 at 110iterations 2.4587732E-02 0.5733919 at 120iterations 1.4102807E-02 0.3008728 at 130iterations 8.0900192E-03 0.1615677 at 140iterations 4.6279258E-03 9.0545654E-02 at 150iterations 2.6454974E-03 5.9392929E-02 at 160iterations 1.5165632E-03 2.9905319E-02 at 170iterations 8.6661265E-04 1.7324448E-02 at 180iterations finished qdiffx linear iterations at : 13:39:01 total time elapsed so far: 15.86000 # loops : 180 mean,max change (kT/e) : 8.6661265E-04 1.7324448E-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) 15.99000 DelPhi exited at 13:39:01 15.990u 0.318s 0:22.04 73.9% 0+0k 0+0io 0pf+0w