Sat Oct 15 15:34:12 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 15:34:12 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2116 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 0.7206478 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): 58.30000 107.7000 ymin,ymax (A): -34.78200 14.49300 zmin,zma (A): 24.77000 70.62400 x,y,z range (A): 49.40000 49.27500 45.85400 scale (grids/A): 0.7206478 object centre (A): 83.00000 -10.14450 47.69700 number of atom coordinates read : 2116 total number of charged atoms : 1986 net assigned charge : 6.039010 assigned positive charge : 327.5161 centred at (gu) : 90.61990 90.54223 89.50665 assigned negative charge : -321.4771 centred at (gu) : 90.53092 90.52201 89.63034 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7614 nv = 96 ne = 84 npr = 41836 no. pairs analyzed = 41836 no. exposed pairs = 2549 no. arc points = 17491 no. surface atoms = 862 nbur = 1254 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 499 mr = 4483 m= 4 mr = 90 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 0.1700000 number of dielectric boundary points 3544 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1627 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8194 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6645949E-07 -1.4933432E-08 midg,1,midg; midg,igrid,midg 4.9438899E-08 9.0801258E-08 1,midg,midg; igrid,midg,midg 6.8749273E-09 1.4443494E-07 gauss-seidel spectral radius is 0.9899632 estimated iterations to convergence 81 setup time was (sec) 0.4100000 now iterating at: 15:34:13 rms-change max change #iterations 0.2258737 28.65665 at 10iterations 2.9379889E-02 4.720461 at 20iterations 4.0600058E-03 0.5301361 at 30iterations 6.7952927E-04 8.7314606E-02 at 40iterations 1.6807851E-04 2.0786285E-02 at 50iterations finished qdiffx linear iterations at : 15:34:18 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 1.6807851E-04 2.0786285E-02 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 15:34:19 3.590u 0.200s 0:06.30 60.1% 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 15:34:19 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2116 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 2.161943 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): 58.30000 107.7000 ymin,ymax (A): -34.78200 14.49300 zmin,zma (A): 24.77000 70.62400 x,y,z range (A): 49.40000 49.27500 45.85400 scale (grids/A): 2.161943 object centre (A): 83.00000 -10.14450 47.69700 number of atom coordinates read : 2116 total number of charged atoms : 1986 net assigned charge : 6.039010 assigned positive charge : 327.5161 centred at (gu) : 91.85976 91.62685 88.52000 assigned negative charge : -321.4771 centred at (gu) : 91.59286 91.56604 88.89101 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79699 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17491 grid for indexing accessible points = 1.400000 m= 33867 mr = 57192 m= 7030 mr = 26306 m= 717 mr = 4809 m= 24 mr = 386 m= 0 mr = 1 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 32643 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 69 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 15774 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) : 0.7206478 object centre at (A) : 83.00000 -10.14450 47.69700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9807105E-02 1.2105144E-02 midg,1,midg; midg,igrid,midg 7.0482962E-02 2.8882114E-02 1,midg,midg; igrid,midg,midg -2.5758287E-02 2.8059274E-02 gauss-seidel spectral radius is 0.9988732 estimated iterations to convergence 236 setup time was (sec) 0.6900000 now iterating at: 15:34:20 rms-change max change #iterations 4.924615 222.6256 at 10iterations 2.466817 79.73221 at 20iterations 1.240441 41.76732 at 30iterations 0.6233293 18.53217 at 40iterations 0.3147549 9.087664 at 50iterations 0.1582576 5.631620 at 60iterations 7.9595417E-02 2.217820 at 70iterations 4.0166475E-02 1.276204 at 80iterations 2.0270457E-02 0.5630875 at 90iterations 1.0268588E-02 0.3012352 at 100iterations 5.2189720E-03 0.1650047 at 110iterations 2.7025377E-03 7.6404572E-02 at 120iterations finished qdiffx linear iterations at : 15:34:34 total time elapsed so far: 8.440000 # loops : 120 mean,max change (kT/e) : 2.7025377E-03 7.6404572E-02 energy calculations done at 8.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.570000 DelPhi exited at 15:34:35 8.576u 0.281s 0:15.72 56.2% 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 Sat Oct 15 2011 at 15:34:35 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2116 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 3.242915 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): 58.30000 107.7000 ymin,ymax (A): -34.78200 14.49300 zmin,zma (A): 24.77000 70.62400 x,y,z range (A): 49.40000 49.27500 45.85400 scale (grids/A): 3.242915 object centre (A): 83.00000 -10.14450 47.69700 number of atom coordinates read : 2116 total number of charged atoms : 1986 net assigned charge : 6.039010 assigned positive charge : 327.5161 centred at (gu) : 92.78965 92.44032 87.77998 assigned negative charge : -321.4771 centred at (gu) : 92.38934 92.34905 88.33662 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 183687 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17491 grid for indexing accessible points = 1.400000 m= 103280 mr = 137413 m= 44813 mr = 86983 m= 13520 mr = 37459 m= 2840 mr = 10618 m= 423 mr = 2126 m= 29 mr = 290 m= 0 mr = 11 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.300000 number of dielectric boundary points 73692 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 15888 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) : 2.161943 object centre at (A) : 83.00000 -10.14450 47.69700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8168870 7.6885782E-02 midg,1,midg; midg,igrid,midg 0.5842381 0.2324447 1,midg,midg; igrid,midg,midg -0.1509050 6.4012304E-02 gauss-seidel spectral radius is 0.9993063 estimated iterations to convergence 300 setup time was (sec) 1.560000 now iterating at: 15:34:37 rms-change max change #iterations 10.75478 362.2167 at 10iterations 6.388344 140.9283 at 20iterations 3.786765 71.18939 at 30iterations 2.235495 39.00509 at 40iterations 1.320397 23.18379 at 50iterations 0.7780659 12.76511 at 60iterations 0.4586854 8.371937 at 70iterations 0.2697800 4.644255 at 80iterations 0.1587988 2.841333 at 90iterations 9.3552403E-02 1.540466 at 100iterations 5.5006549E-02 1.021465 at 110iterations 3.2477137E-02 0.5511436 at 120iterations 1.9275760E-02 0.3217125 at 130iterations 1.1569795E-02 0.2170181 at 140iterations 7.0766872E-03 0.1239090 at 150iterations 4.4591287E-03 7.3798180E-02 at 160iterations 2.9441228E-03 4.7990799E-02 at 170iterations 2.0619889E-03 3.4313202E-02 at 180iterations finished qdiffx linear iterations at : 15:34:59 total time elapsed so far: 14.37000 # loops : 180 mean,max change (kT/e) : 2.0619889E-03 3.4313202E-02 energy calculations done at 14.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.51000 DelPhi exited at 15:35:00 14.507u 0.284s 0:24.85 59.4% 0+0k 0+0io 0pf+0w