Tue Oct 11 04:31:03 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 04:31:03 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2770 !!! WARNING: ASP 29 has a net charge of -2.0000 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6563542 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): -11.71000 37.14700 ymin,ymax (A): -25.77500 22.59600 zmin,zma (A): -8.833000 45.40600 x,y,z range (A): 48.85700 48.37100 54.23900 scale (grids/A): 0.6563542 object centre (A): 12.71850 -1.589500 18.28650 number of atom coordinates read : 2770 total number of charged atoms : 2618 net assigned charge : -0.8239793 assigned positive charge : 420.0677 centred at (gu) : 90.15956 90.42201 91.53453 assigned negative charge : -420.8923 centred at (gu) : 89.90523 90.30703 91.49543 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7838 nv = 96 ne = 84 npr = 56925 no. pairs analyzed = 56925 no. exposed pairs = 3397 no. arc points = 23361 no. surface atoms = 1148 nbur = 1622 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 439 mr = 4421 m= 3 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.2100000 number of dielectric boundary points 3801 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2321 ## 224 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9494 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.0992745E-09 7.6432709E-09 midg,1,midg; midg,igrid,midg -2.2698753E-08 2.1907251E-08 1,midg,midg; igrid,midg,midg -5.1307538E-08 4.7724239E-08 gauss-seidel spectral radius is 0.9879811 estimated iterations to convergence 74 setup time was (sec) 0.4100000 now iterating at: 04:31:04 rms-change max change #iterations 0.1688827 22.89485 at 10iterations 1.8401440E-02 2.506577 at 20iterations 2.0736333E-03 0.2953644 at 30iterations 3.1367133E-04 4.1053772E-02 at 40iterations 7.7469122E-05 9.0923309E-03 at 50iterations finished qdiffx linear iterations at : 04:31:07 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 7.7469122E-05 9.0923309E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 04:31:07 3.430u 0.169s 0:04.15 86.5% 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 Tue Oct 11 2011 at 04:31:07 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2770 !!! WARNING: ASP 29 has a net charge of -2.0000 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.969063 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): -11.71000 37.14700 ymin,ymax (A): -25.77500 22.59600 zmin,zma (A): -8.833000 45.40600 x,y,z range (A): 48.85700 48.37100 54.23900 scale (grids/A): 1.969063 object centre (A): 12.71850 -1.589500 18.28650 number of atom coordinates read : 2770 total number of charged atoms : 2618 net assigned charge : -0.8239793 assigned positive charge : 420.0677 centred at (gu) : 90.47826 91.26540 94.60288 assigned negative charge : -420.8923 centred at (gu) : 89.71545 90.92081 94.48608 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 85006 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23361 grid for indexing accessible points = 1.400000 m= 31774 mr = 60032 m= 5121 mr = 23801 m= 315 mr = 3244 m= 4 mr = 127 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1106 time to turn everything in is 0.4200000 number of dielectric boundary points 35016 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 20661 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) : 0.6563542 object centre at (A) : 12.71850 -1.589500 18.28650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.0309073E-02 -2.2880010E-02 midg,1,midg; midg,igrid,midg -1.4990980E-02 2.1453045E-02 1,midg,midg; igrid,midg,midg -1.7169289E-02 6.7544147E-02 gauss-seidel spectral radius is 0.9987336 estimated iterations to convergence 223 setup time was (sec) 0.6300000 now iterating at: 04:31:08 rms-change max change #iterations 4.764987 188.1784 at 10iterations 2.298533 77.81201 at 20iterations 1.105042 36.12346 at 30iterations 0.5339150 16.72735 at 40iterations 0.2592123 7.121920 at 50iterations 0.1251445 3.594387 at 60iterations 6.0101934E-02 1.728833 at 70iterations 2.9134750E-02 0.9004116 at 80iterations 1.4095231E-02 0.3965240 at 90iterations 6.8434379E-03 0.2195907 at 100iterations 3.3418273E-03 9.3368530E-02 at 110iterations 1.6437293E-03 4.4492722E-02 at 120iterations finished qdiffx linear iterations at : 04:31:15 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 1.6437293E-03 4.4492722E-02 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 04:31:16 7.918u 0.206s 0:08.66 93.6% 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 04:31:16 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2770 !!! WARNING: ASP 29 has a net charge of -2.0000 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.953594 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): -11.71000 37.14700 ymin,ymax (A): -25.77500 22.59600 zmin,zma (A): -8.833000 45.40600 x,y,z range (A): 48.85700 48.37100 54.23900 scale (grids/A): 2.953594 object centre (A): 12.71850 -1.589500 18.28650 number of atom coordinates read : 2770 total number of charged atoms : 2618 net assigned charge : -0.8239793 assigned positive charge : 420.0677 centred at (gu) : 90.71726 91.89795 96.90423 assigned negative charge : -420.8923 centred at (gu) : 89.57306 91.38111 96.72896 start vw surface at 0.1000000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 196279 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23361 grid for indexing accessible points = 1.400000 m= 102159 mr = 144865 m= 38057 mr = 84466 m= 9298 mr = 30875 m= 1300 mr = 6981 m= 98 mr = 869 m= 2 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 3937 time to turn everything in is 1.110000 number of dielectric boundary points 79092 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 20938 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) : 1.969063 object centre at (A) : 12.71850 -1.589500 18.28650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.351035 0.1088407 midg,1,midg; midg,igrid,midg -0.1651710 0.2840590 1,midg,midg; igrid,midg,midg -0.1205130 0.6177335 gauss-seidel spectral radius is 0.9992827 estimated iterations to convergence 295 setup time was (sec) 1.340000 now iterating at: 04:31:18 rms-change max change #iterations 10.94267 341.1815 at 10iterations 6.421278 169.6215 at 20iterations 3.763343 73.07798 at 30iterations 2.203254 42.71003 at 40iterations 1.288312 26.19921 at 50iterations 0.7531914 14.14492 at 60iterations 0.4382355 7.798291 at 70iterations 0.2552368 4.300392 at 80iterations 0.1486141 2.791779 at 90iterations 8.6476400E-02 1.456877 at 100iterations 5.0446890E-02 0.9093323 at 110iterations 2.9453659E-02 0.4718857 at 120iterations 1.7152796E-02 0.3084469 at 130iterations 1.0042798E-02 0.1742096 at 140iterations 5.9214295E-03 0.1051731 at 150iterations 3.5460773E-03 6.6438675E-02 at 160iterations 2.1604267E-03 4.4113159E-02 at 170iterations 1.3573969E-03 2.8766632E-02 at 180iterations finished qdiffx linear iterations at : 04:31:29 total time elapsed so far: 12.81000 # loops : 180 mean,max change (kT/e) : 1.3573969E-03 2.8766632E-02 energy calculations done at 12.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.95000 DelPhi exited at 04:31:30 12.949u 0.207s 0:13.54 97.0% 0+0k 0+0io 0pf+0w