Mon Oct 10 14:04:06 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 Mon Oct 10 2011 at 14:04:06 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5176 !!! WARNING: HIZ 652 has a net charge of 0.2000 !!! WARNING: ZN7 714 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5181951 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): 24.42400 85.03400 ymin,ymax (A): 15.12900 82.45600 zmin,zma (A): -35.09500 33.60500 x,y,z range (A): 60.61000 67.32700 68.70000 scale (grids/A): 0.5181951 object centre (A): 54.72900 48.79250 -0.7449989 number of atom coordinates read : 5176 total number of charged atoms : 5006 net assigned charge : -1.399960 assigned positive charge : 792.5569 centred at (gu) : 90.72255 89.81422 90.60129 assigned negative charge : -793.9633 centred at (gu) : 90.65192 89.86016 90.64162 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8479 nv = 96 ne = 84 npr = 106908 no. pairs analyzed = 106908 no. exposed pairs = 5936 no. arc points = 40536 no. surface atoms = 2018 nbur = 3158 mkacc time = 0.2300000 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 = 1.652000 m= 300 mr = 4683 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.4700000 number of dielectric boundary points 4081 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3984 ## 588 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 11503 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1087691E-10 -2.2293943E-10 midg,1,midg; midg,igrid,midg 1.5982270E-10 -2.0267459E-10 1,midg,midg; igrid,midg,midg -2.5845961E-10 3.0139230E-10 gauss-seidel spectral radius is 0.9809670 estimated iterations to convergence 60 setup time was (sec) 0.6900000 now iterating at: 14:04:07 rms-change max change #iterations 7.8075379E-02 10.97942 at 10iterations 7.1520070E-03 1.223419 at 20iterations 1.8534317E-03 0.3400230 at 30iterations 6.0724723E-04 0.1132698 at 40iterations 1.9991692E-04 3.7563324E-02 at 50iterations finished qdiffx linear iterations at : 14:04:09 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 1.9991692E-04 3.7563324E-02 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 14:04:10 3.284u 0.130s 0:03.83 89.0% 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 Mon Oct 10 2011 at 14:04:10 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5176 !!! WARNING: HIZ 652 has a net charge of 0.2000 !!! WARNING: ZN7 714 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.554585 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): 24.42400 85.03400 ymin,ymax (A): 15.12900 82.45600 zmin,zma (A): -35.09500 33.60500 x,y,z range (A): 60.61000 67.32700 68.70000 scale (grids/A): 1.554585 object centre (A): 54.72900 48.79250 -0.7449989 number of atom coordinates read : 5176 total number of charged atoms : 5006 net assigned charge : -1.399960 assigned positive charge : 792.5569 centred at (gu) : 92.16616 89.44142 91.80209 assigned negative charge : -793.9633 centred at (gu) : 91.95557 89.57998 91.92436 start vw surface at 0.2200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 96460 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40536 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 28734 mr = 68308 m= 2616 mr = 20137 m= 60 mr = 1306 m= 0 mr = 4 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1935 time to turn everything in is 0.6700000 number of dielectric boundary points 38115 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 515 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 37759 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) : 0.5181951 object centre at (A) : 54.72900 48.79250 -0.7449989 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1807000E-02 4.2310415E-04 midg,1,midg; midg,igrid,midg 2.2301644E-02 -1.7689534E-02 1,midg,midg; igrid,midg,midg -7.1989461E-03 1.5834907E-02 gauss-seidel spectral radius is 0.9981912 estimated iterations to convergence 187 setup time was (sec) 0.9200000 now iterating at: 14:04:11 rms-change max change #iterations 4.147412 154.2223 at 10iterations 1.736037 56.35324 at 20iterations 0.7289468 24.20698 at 30iterations 0.3064058 10.07119 at 40iterations 0.1282049 4.356936 at 50iterations 5.4273706E-02 1.578373 at 60iterations 2.3095120E-02 0.7350101 at 70iterations 1.0110414E-02 0.3225861 at 80iterations 4.6509290E-03 0.1559753 at 90iterations 2.3322226E-03 8.3648682E-02 at 100iterations 1.2860079E-03 4.8568726E-02 at 110iterations 7.7060767E-04 2.7503967E-02 at 120iterations finished qdiffx linear iterations at : 14:04:17 total time elapsed so far: 6.860000 # loops : 120 mean,max change (kT/e) : 7.7060767E-04 2.7503967E-02 energy calculations done at 6.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.050000 DelPhi exited at 14:04:18 7.052u 0.199s 0:07.94 91.1% 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 Mon Oct 10 2011 at 14:04:18 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5176 !!! WARNING: HIZ 652 has a net charge of 0.2000 !!! WARNING: ZN7 714 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.331878 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): 24.42400 85.03400 ymin,ymax (A): 15.12900 82.45600 zmin,zma (A): -35.09500 33.60500 x,y,z range (A): 60.61000 67.32700 68.70000 scale (grids/A): 2.331878 object centre (A): 54.72900 48.79250 -0.7449989 number of atom coordinates read : 5176 total number of charged atoms : 5006 net assigned charge : -1.399960 assigned positive charge : 792.5569 centred at (gu) : 93.24888 89.16176 92.70274 assigned negative charge : -793.9633 centred at (gu) : 92.93318 89.37006 92.88692 start vw surface at 0.2100000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 225026 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40536 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 102070 mr = 167271 m= 27057 mr = 81792 m= 3894 mr = 20507 m= 233 mr = 2540 m= 6 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 6816 time to turn everything in is 1.530000 number of dielectric boundary points 86082 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 51 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 39955 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) : 1.554585 object centre at (A) : 54.72900 48.79250 -0.7449989 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2321707 0.1066130 midg,1,midg; midg,igrid,midg 0.4228714 -0.3928693 1,midg,midg; igrid,midg,midg -8.7100536E-02 0.4293188 gauss-seidel spectral radius is 0.9991840 estimated iterations to convergence 276 setup time was (sec) 1.810000 now iterating at: 14:04:20 rms-change max change #iterations 10.99594 294.8226 at 10iterations 6.325476 132.3690 at 20iterations 3.598303 78.53249 at 30iterations 2.041590 42.67883 at 40iterations 1.154415 21.73011 at 50iterations 0.6495333 12.68029 at 60iterations 0.3662494 6.528862 at 70iterations 0.2062554 3.676392 at 80iterations 0.1156451 2.114559 at 90iterations 6.4836733E-02 1.138582 at 100iterations 3.6388714E-02 0.7811890 at 110iterations 2.0373242E-02 0.3592072 at 120iterations 1.1464744E-02 0.1941795 at 130iterations 6.4870049E-03 0.1128311 at 140iterations 3.6832541E-03 7.1693420E-02 at 150iterations 2.1143313E-03 3.8417816E-02 at 160iterations 1.2391253E-03 2.3679733E-02 at 170iterations 7.4977725E-04 1.4934540E-02 at 180iterations finished qdiffx linear iterations at : 14:04:30 total time elapsed so far: 11.35000 # loops : 180 mean,max change (kT/e) : 7.4977725E-04 1.4934540E-02 energy calculations done at 11.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.53000 DelPhi exited at 14:04:30 11.535u 0.165s 0:12.13 96.3% 0+0k 0+0io 0pf+0w