Tue Nov 22 14:11:05 PST 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 Nov 22 2011 at 14:11:12 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 = 1964 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: 0.6432611 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): -6.316000 34.94700 ymin,ymax (A): -3.660000 50.00600 zmin,zma (A): -24.38700 30.95600 x,y,z range (A): 41.26300 53.66600 55.34300 scale (grids/A): 0.6432611 object centre (A): 14.31550 23.17300 3.284501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 90.98782 92.16389 90.22195 assigned negative charge : -284.8263 centred at (gu) : 91.09490 92.29607 90.15408 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5599 nv = 96 ne = 84 npr = 40146 no. pairs analyzed = 40146 no. exposed pairs = 2411 no. arc points = 17062 no. surface atoms = 816 nbur = 1148 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 305 mr = 3174 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.2100000 number of dielectric boundary points 2696 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1694 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 6489 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1052028E-09 1.1982269E-08 midg,1,midg; midg,igrid,midg 1.0940027E-08 -1.1925476E-08 1,midg,midg; igrid,midg,midg 1.2167238E-08 -6.1328760E-09 gauss-seidel spectral radius is 0.9874229 estimated iterations to convergence 73 setup time was (sec) 0.4300000 now iterating at: 14:11:16 rms-change max change #iterations 0.1255945 20.26531 at 10iterations 1.2459786E-02 1.970531 at 20iterations 1.2373822E-03 0.1862952 at 30iterations 1.2470501E-04 1.7923355E-02 at 40iterations 1.2334714E-05 2.0484924E-03 at 50iterations finished qdiffx linear iterations at : 14:11:23 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 1.2334714E-05 2.0484924E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 14:11:25 3.108u 0.165s 0:14.67 22.2% 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 Nov 22 2011 at 14:11:28 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 = 1964 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: 1.929783 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): -6.316000 34.94700 ymin,ymax (A): -3.660000 50.00600 zmin,zma (A): -24.38700 30.95600 x,y,z range (A): 41.26300 53.66600 55.34300 scale (grids/A): 1.929783 object centre (A): 14.31550 23.17300 3.284501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 92.96365 96.49184 90.66580 assigned negative charge : -284.8263 centred at (gu) : 93.28496 96.88840 90.46247 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 59877 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17062 grid for indexing accessible points = 1.400000 m= 22112 mr = 41508 m= 3401 mr = 16988 m= 181 mr = 2199 m= 7 mr = 61 m= 0 mr = 4 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 2696 time to turn everything in is 0.4300000 number of dielectric boundary points 24818 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 134 iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 14453 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) : 0.6432611 object centre at (A) : 14.31550 23.17300 3.284501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9372697E-02 1.8883985E-02 midg,1,midg; midg,igrid,midg 3.6355235E-02 -1.0857725E-02 1,midg,midg; igrid,midg,midg 9.0003219E-03 -3.6633674E-03 gauss-seidel spectral radius is 0.9985915 estimated iterations to convergence 211 setup time was (sec) 0.7100000 now iterating at: 14:11:33 rms-change max change #iterations 3.634476 169.8042 at 10iterations 1.688011 78.02544 at 20iterations 0.7826557 28.42331 at 30iterations 0.3627701 14.23359 at 40iterations 0.1677782 5.842522 at 50iterations 7.7205256E-02 2.656133 at 60iterations 3.5759911E-02 1.190948 at 70iterations 1.6533028E-02 0.5467272 at 80iterations 7.6351138E-03 0.2649469 at 90iterations 3.5536848E-03 0.1227112 at 100iterations 1.6460906E-03 5.8383703E-02 at 110iterations 7.6094322E-04 2.7404785E-02 at 120iterations finished qdiffx linear iterations at : 14:11:53 total time elapsed so far: 7.070000 # loops : 120 mean,max change (kT/e) : 7.6094322E-04 2.7404785E-02 energy calculations done at 7.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.240000 DelPhi exited at 14:11:56 7.244u 0.180s 0:28.30 26.2% 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 Nov 22 2011 at 14:11:58 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 = 1964 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: 2.894675 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): -6.316000 34.94700 ymin,ymax (A): -3.660000 50.00600 zmin,zma (A): -24.38700 30.95600 x,y,z range (A): 41.26300 53.66600 55.34300 scale (grids/A): 2.894675 object centre (A): 14.31550 23.17300 3.284501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 94.44540 99.73774 90.99869 assigned negative charge : -284.8263 centred at (gu) : 94.92754 100.3326 90.69373 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 138521 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17062 grid for indexing accessible points = 1.400000 m= 71292 mr = 100502 m= 26275 mr = 59397 m= 5985 mr = 21811 m= 770 mr = 4650 m= 48 mr = 508 m= 5 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 8933 time to turn everything in is 1.050000 number of dielectric boundary points 55996 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 14656 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) : 1.929783 object centre at (A) : 14.31550 23.17300 3.284501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9846494 5.5420376E-02 midg,1,midg; midg,igrid,midg 0.3757652 -0.1480969 1,midg,midg; igrid,midg,midg 5.3318959E-02 -1.3999807E-02 gauss-seidel spectral radius is 0.9992318 estimated iterations to convergence 285 setup time was (sec) 1.350000 now iterating at: 14:12:06 rms-change max change #iterations 8.458942 308.7826 at 10iterations 4.821040 126.7447 at 20iterations 2.728237 56.22775 at 30iterations 1.547425 30.54061 at 40iterations 0.8816797 17.57797 at 50iterations 0.4989185 9.950741 at 60iterations 0.2828184 5.916336 at 70iterations 0.1606559 3.067078 at 80iterations 9.1000177E-02 1.821220 at 90iterations 5.1705554E-02 1.001820 at 100iterations 2.9320594E-02 0.5906439 at 110iterations 1.6634636E-02 0.3446236 at 120iterations 9.4133150E-03 0.2298050 at 130iterations 5.3371033E-03 0.1007538 at 140iterations 3.0301174E-03 6.1384201E-02 at 150iterations 1.7223991E-03 3.7440300E-02 at 160iterations 9.7557000E-04 2.1053314E-02 at 170iterations 5.5357523E-04 1.0862827E-02 at 180iterations finished qdiffx linear iterations at : 14:12:38 total time elapsed so far: 11.38000 # loops : 180 mean,max change (kT/e) : 5.5357523E-04 1.0862827E-02 energy calculations done at 11.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.56000 DelPhi exited at 14:12:42 11.559u 0.223s 0:43.79 26.8% 0+0k 0+0io 0pf+0w