Sat Oct 15 13:42:27 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 Sat Oct 15 2011 at 13:42:27 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 = 3282 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: 0.5499004 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): -57.41900 6.688000 ymin,ymax (A): 23.66200 88.40100 zmin,zma (A): -25.08200 23.92500 x,y,z range (A): 64.10699 64.73900 49.00700 scale (grids/A): 0.5499004 object centre (A): -25.36550 56.03150 -0.5784998 number of atom coordinates read : 3282 total number of charged atoms : 3122 net assigned charge : -9.499988 assigned positive charge : 502.2973 centred at (gu) : 89.48585 90.50652 90.03352 assigned negative charge : -511.7987 centred at (gu) : 89.52157 90.54294 90.01308 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6550 nv = 96 ne = 84 npr = 62399 no. pairs analyzed = 62399 no. exposed pairs = 4752 no. arc points = 34348 no. surface atoms = 1552 nbur = 1730 mkacc time = 9.9999994E-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 = 1.568000 m= 300 mr = 2986 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3846 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3433 ## 457 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 8596 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.6340246E-10 -5.1251792E-10 midg,1,midg; midg,igrid,midg -3.2795178E-10 -1.1455699E-09 1,midg,midg; igrid,midg,midg -4.2101495E-10 -8.8910407E-10 gauss-seidel spectral radius is 0.9829882 estimated iterations to convergence 63 setup time was (sec) 0.4800000 now iterating at: 13:42:28 rms-change max change #iterations 8.0410175E-02 14.72446 at 10iterations 5.3663133E-03 0.8390989 at 20iterations 4.7765553E-04 9.2024803E-02 at 30iterations 1.1019000E-04 3.0040741E-02 at 40iterations 3.6496542E-05 1.0250092E-02 at 50iterations finished qdiffx linear iterations at : 13:42:35 total time elapsed so far: 3.580000 # loops : 50 mean,max change (kT/e) : 3.6496542E-05 1.0250092E-02 energy calculations done at 3.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.710000 DelPhi exited at 13:42:35 3.717u 0.232s 0:08.81 44.7% 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 Sat Oct 15 2011 at 13:42:36 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 = 3282 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.649701 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): -57.41900 6.688000 ymin,ymax (A): 23.66200 88.40100 zmin,zma (A): -25.08200 23.92500 x,y,z range (A): 64.10699 64.73900 49.00700 scale (grids/A): 1.649701 object centre (A): -25.36550 56.03150 -0.5784998 number of atom coordinates read : 3282 total number of charged atoms : 3122 net assigned charge : -9.499988 assigned positive charge : 502.2973 centred at (gu) : 88.45663 91.51881 90.09962 assigned negative charge : -511.7987 centred at (gu) : 88.56436 91.62821 90.03881 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 72308 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34348 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 21382 mr = 45570 m= 2409 mr = 13640 m= 98 mr = 1111 m= 0 mr = 13 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 859 time to turn everything in is 0.4000000 number of dielectric boundary points 35863 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 328 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 23975 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) : 0.5499004 object centre at (A) : -25.36550 56.03150 -0.5784998 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.2045460E-03 -5.8935530E-05 midg,1,midg; midg,igrid,midg 1.6894093E-03 -1.5120627E-02 1,midg,midg; igrid,midg,midg -1.6345022E-02 -2.2939013E-02 gauss-seidel spectral radius is 0.9982768 estimated iterations to convergence 191 setup time was (sec) 0.6600000 now iterating at: 13:42:37 rms-change max change #iterations 3.667095 196.1661 at 10iterations 1.552655 57.53966 at 20iterations 0.6593501 23.13366 at 30iterations 0.2801599 9.951384 at 40iterations 0.1193721 4.115379 at 50iterations 5.0691217E-02 1.677085 at 60iterations 2.1514632E-02 0.8303204 at 70iterations 9.1999061E-03 0.3504858 at 80iterations 3.9303857E-03 0.1457367 at 90iterations 1.6993566E-03 5.9594154E-02 at 100iterations 7.5102568E-04 3.0515671E-02 at 110iterations 3.4659958E-04 1.4724731E-02 at 120iterations finished qdiffx linear iterations at : 13:42:50 total time elapsed so far: 9.080000 # loops : 120 mean,max change (kT/e) : 3.4659958E-04 1.4724731E-02 energy calculations done at 9.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.210000 DelPhi exited at 13:42:50 9.217u 0.285s 0:14.47 65.5% 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 13:42:50 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 = 3282 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: 2.474552 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): -57.41900 6.688000 ymin,ymax (A): 23.66200 88.40100 zmin,zma (A): -25.08200 23.92500 x,y,z range (A): 64.10699 64.73900 49.00700 scale (grids/A): 2.474552 object centre (A): -25.36550 56.03150 -0.5784998 number of atom coordinates read : 3282 total number of charged atoms : 3122 net assigned charge : -9.499988 assigned positive charge : 502.2973 centred at (gu) : 87.68449 92.27802 90.14934 assigned negative charge : -511.7987 centred at (gu) : 87.84640 92.44221 90.05811 start vw surface at 0.1000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 167739 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34348 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 73264 mr = 112526 m= 20960 mr = 55307 m= 3818 mr = 14796 m= 388 mr = 2431 m= 14 mr = 180 m= 0 mr = 1 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 2743 time to turn everything in is 0.9000000 number of dielectric boundary points 80942 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 24948 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) : 1.649701 object centre at (A) : -25.36550 56.03150 -0.5784998 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1267196 6.0673766E-02 midg,1,midg; midg,igrid,midg 0.1409511 -0.1138017 1,midg,midg; igrid,midg,midg -0.5291089 -0.2995988 gauss-seidel spectral radius is 0.9991844 estimated iterations to convergence 277 setup time was (sec) 1.160000 now iterating at: 13:42:52 rms-change max change #iterations 9.625598 346.6841 at 10iterations 5.542708 157.8594 at 20iterations 3.157444 75.07487 at 30iterations 1.793486 41.89784 at 40iterations 1.013084 22.57676 at 50iterations 0.5703258 11.74529 at 60iterations 0.3210446 7.268849 at 70iterations 0.1800656 3.681862 at 80iterations 0.1008864 2.078620 at 90iterations 5.6432419E-02 1.132778 at 100iterations 3.1542573E-02 0.6260281 at 110iterations 1.7696340E-02 0.4045601 at 120iterations 9.8376563E-03 0.2157240 at 130iterations 5.5078552E-03 0.1112938 at 140iterations 3.0771997E-03 6.1158180E-02 at 150iterations 1.7213289E-03 3.4332275E-02 at 160iterations 9.5997116E-04 1.7667770E-02 at 170iterations 5.3510326E-04 1.1628628E-02 at 180iterations finished qdiffx linear iterations at : 13:43:07 total time elapsed so far: 13.52000 # loops : 180 mean,max change (kT/e) : 5.3510326E-04 1.1628628E-02 energy calculations done at 13.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.65000 DelPhi exited at 13:43:08 13.652u 0.230s 0:17.40 79.7% 0+0k 0+0io 0pf+0w