Tue Oct 11 06:20:02 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 06:20:02 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 = 2076 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6939706 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): -9.811000 36.70900 ymin,ymax (A): -3.245000 34.80500 zmin,zma (A): 0.2110000 51.51000 x,y,z range (A): 46.52000 38.05000 51.29900 scale (grids/A): 0.6939706 object centre (A): 13.44900 15.78000 25.86050 number of atom coordinates read : 2076 total number of charged atoms : 1947 net assigned charge : 5.500006 assigned positive charge : 315.3210 centred at (gu) : 89.51975 89.26086 90.18006 assigned negative charge : -309.8212 centred at (gu) : 89.41213 89.32771 90.20974 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6694 nv = 96 ne = 84 npr = 42224 no. pairs analyzed = 42224 no. exposed pairs = 2431 no. arc points = 16728 no. surface atoms = 829 nbur = 1247 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 434 mr = 3865 m= 2 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3170 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1629 ## 151 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7612 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2767049E-08 2.3617305E-08 midg,1,midg; midg,igrid,midg 6.6619734E-08 8.2446947E-09 1,midg,midg; igrid,midg,midg -6.5238401E-09 6.5556890E-08 gauss-seidel spectral radius is 0.9891773 estimated iterations to convergence 78 setup time was (sec) 0.3700000 now iterating at: 06:20:03 rms-change max change #iterations 0.1892816 25.99282 at 10iterations 2.2327330E-02 2.854250 at 20iterations 2.8250169E-03 0.3912430 at 30iterations 4.2777119E-04 5.4996490E-02 at 40iterations 9.4487325E-05 1.1722565E-02 at 50iterations finished qdiffx linear iterations at : 06:20:06 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 9.4487325E-05 1.1722565E-02 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 06:20:06 3.473u 0.185s 0:04.01 91.0% 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 Tue Oct 11 2011 at 06:20:06 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 = 2076 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.081912 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): -9.811000 36.70900 ymin,ymax (A): -3.245000 34.80500 zmin,zma (A): 0.2110000 51.51000 x,y,z range (A): 46.52000 38.05000 51.29900 scale (grids/A): 2.081912 object centre (A): 13.44900 15.78000 25.86050 number of atom coordinates read : 2076 total number of charged atoms : 1947 net assigned charge : 5.500006 assigned positive charge : 315.3210 centred at (gu) : 88.55921 87.78226 90.54003 assigned negative charge : -309.8212 centred at (gu) : 88.23638 87.98320 90.62920 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 71778 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16728 grid for indexing accessible points = 1.400000 m= 28198 mr = 51357 m= 5187 mr = 21342 m= 425 mr = 3399 m= 7 mr = 212 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 29285 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 84 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 15427 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) : 0.6939706 object centre at (A) : 13.44900 15.78000 25.86050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0328171E-02 4.1277144E-02 midg,1,midg; midg,igrid,midg 3.1641651E-02 -2.2503044E-03 1,midg,midg; igrid,midg,midg 1.6359324E-02 2.5908625E-02 gauss-seidel spectral radius is 0.9987866 estimated iterations to convergence 227 setup time was (sec) 0.5900000 now iterating at: 06:20:07 rms-change max change #iterations 4.458870 217.9808 at 10iterations 2.176471 71.59574 at 20iterations 1.065040 36.23456 at 30iterations 0.5252135 16.10178 at 40iterations 0.2569958 7.685130 at 50iterations 0.1258695 3.781116 at 60iterations 6.1849400E-02 1.848503 at 70iterations 3.0406393E-02 0.9283400 at 80iterations 1.4954585E-02 0.5354500 at 90iterations 7.3920279E-03 0.2301941 at 100iterations 3.6683022E-03 0.1370583 at 110iterations 1.8510375E-03 5.6783676E-02 at 120iterations finished qdiffx linear iterations at : 06:20:14 total time elapsed so far: 7.860000 # loops : 120 mean,max change (kT/e) : 1.8510375E-03 5.6783676E-02 energy calculations done at 7.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 06:20:15 7.999u 0.211s 0:08.79 93.2% 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 06:20:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2076 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.122868 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): -9.811000 36.70900 ymin,ymax (A): -3.245000 34.80500 zmin,zma (A): 0.2110000 51.51000 x,y,z range (A): 46.52000 38.05000 51.29900 scale (grids/A): 3.122868 object centre (A): 13.44900 15.78000 25.86050 number of atom coordinates read : 2076 total number of charged atoms : 1947 net assigned charge : 5.500006 assigned positive charge : 315.3210 centred at (gu) : 87.83884 86.67347 90.80994 assigned negative charge : -309.8212 centred at (gu) : 87.35463 86.97469 90.94388 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 165754 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16728 grid for indexing accessible points = 1.400000 m= 89341 mr = 123857 m= 34918 mr = 74409 m= 9556 mr = 28575 m= 1750 mr = 7346 m= 217 mr = 1242 m= 7 mr = 139 m= 0 mr = 0 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.090000 number of dielectric boundary points 65975 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 15572 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) : 2.081912 object centre at (A) : 13.44900 15.78000 25.86050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3462797 0.3716034 midg,1,midg; midg,igrid,midg 0.2788200 -1.0533736E-02 1,midg,midg; igrid,midg,midg 0.2780767 0.2436345 gauss-seidel spectral radius is 0.9992802 estimated iterations to convergence 294 setup time was (sec) 1.340000 now iterating at: 06:20:17 rms-change max change #iterations 10.02033 334.6183 at 10iterations 5.892089 207.3435 at 20iterations 3.459836 68.04667 at 30iterations 2.028105 42.59737 at 40iterations 1.187271 22.90975 at 50iterations 0.6931258 13.10535 at 60iterations 0.4043505 7.886752 at 70iterations 0.2360952 4.286743 at 80iterations 0.1373696 2.405785 at 90iterations 8.0144383E-02 1.493958 at 100iterations 4.6684846E-02 0.8758068 at 110iterations 2.7352154E-02 0.4794540 at 120iterations 1.6060932E-02 0.2873955 at 130iterations 9.5525431E-03 0.1670074 at 140iterations 5.7605272E-03 0.1155548 at 150iterations 3.5765923E-03 7.3268890E-02 at 160iterations 2.3240112E-03 4.3380737E-02 at 170iterations 1.5967313E-03 3.1387329E-02 at 180iterations finished qdiffx linear iterations at : 06:20:28 total time elapsed so far: 13.05000 # loops : 180 mean,max change (kT/e) : 1.5967313E-03 3.1387329E-02 energy calculations done at 13.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.19000 DelPhi exited at 06:20:29 13.188u 0.223s 0:13.79 97.1% 0+0k 0+0io 0pf+0w