Sat Oct 15 13:39:58 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 13:39:58 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5597 !!! WARNING: HIR 312 has a net charge of 0.5140 !!! WARNING: HIT 421 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.4913666 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): -22.07500 45.20800 ymin,ymax (A): -27.50600 41.79000 zmin,zma (A): 5.942000 78.39300 x,y,z range (A): 67.28300 69.29600 72.45100 scale (grids/A): 0.4913666 object centre (A): 11.56650 7.141998 42.16750 number of atom coordinates read : 5597 total number of charged atoms : 5440 net assigned charge : 13.02802 assigned positive charge : 890.8789 centred at (gu) : 91.01403 90.43750 87.90457 assigned negative charge : -877.8596 centred at (gu) : 91.03715 90.40771 87.87386 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8561 nv = 96 ne = 84 npr = 110296 no. pairs analyzed = 110296 no. exposed pairs = 6581 no. arc points = 45340 no. surface atoms = 2213 nbur = 3384 mkacc time = 0.1900000 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 = 1.764000 m= 272 mr = 4709 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3700000 number of dielectric boundary points 4117 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4370 ## 697 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 11484 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.9403808E-11 6.7287127E-11 midg,1,midg; midg,igrid,midg 3.2343746E-11 1.3093328E-10 1,midg,midg; igrid,midg,midg 8.1909653E-11 5.8732436E-11 gauss-seidel spectral radius is 0.9788774 estimated iterations to convergence 57 setup time was (sec) 0.5600000 now iterating at: 13:39:58 rms-change max change #iterations 6.2655777E-02 9.765877 at 10iterations 3.7857150E-03 0.5463829 at 20iterations 9.8371366E-04 0.1484888 at 30iterations 4.9280672E-04 7.8251362E-02 at 40iterations 2.5502645E-04 4.0897846E-02 at 50iterations finished qdiffx linear iterations at : 13:40:02 total time elapsed so far: 3.590000 # loops : 50 mean,max change (kT/e) : 2.5502645E-04 4.0897846E-02 energy calculations done at 3.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.720000 DelPhi exited at 13:40:02 3.726u 0.193s 0:04.70 83.1% 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 13:40:02 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5597 !!! WARNING: HIR 312 has a net charge of 0.5140 !!! WARNING: HIT 421 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.474100 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): -22.07500 45.20800 ymin,ymax (A): -27.50600 41.79000 zmin,zma (A): 5.942000 78.39300 x,y,z range (A): 67.28300 69.29600 72.45100 scale (grids/A): 1.474100 object centre (A): 11.56650 7.141998 42.16750 number of atom coordinates read : 5597 total number of charged atoms : 5440 net assigned charge : 13.02802 assigned positive charge : 890.8789 centred at (gu) : 93.04003 91.31089 83.71195 assigned negative charge : -877.8596 centred at (gu) : 93.11176 91.22292 83.62151 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 98474 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45340 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 27764 mr = 70071 m= 2115 mr = 18825 m= 32 mr = 853 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 2826 time to turn everything in is 0.4600000 number of dielectric boundary points 38636 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 704 ## 14 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 40260 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) : 0.4913666 object centre at (A) : 11.56650 7.141998 42.16750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2710625E-03 4.0586600E-03 midg,1,midg; midg,igrid,midg -1.4713904E-02 8.2539236E-03 1,midg,midg; igrid,midg,midg 1.2237138E-02 3.7445074E-03 gauss-seidel spectral radius is 0.9979966 estimated iterations to convergence 178 setup time was (sec) 0.6700000 now iterating at: 13:40:03 rms-change max change #iterations 3.917433 155.1079 at 10iterations 1.558524 53.14609 at 20iterations 0.6236041 19.64999 at 30iterations 0.2500446 8.572414 at 40iterations 9.9812500E-02 3.649981 at 50iterations 4.0029943E-02 1.265423 at 60iterations 1.6127095E-02 0.5121059 at 70iterations 6.6919043E-03 0.2257004 at 80iterations 2.9739642E-03 0.1090908 at 90iterations 1.5605038E-03 5.3274632E-02 at 100iterations 1.0065957E-03 3.4869194E-02 at 110iterations 7.4429868E-04 2.4295807E-02 at 120iterations finished qdiffx linear iterations at : 13:40:14 total time elapsed so far: 8.410000 # loops : 120 mean,max change (kT/e) : 7.4429868E-04 2.4295807E-02 energy calculations done at 8.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.540000 DelPhi exited at 13:40:15 8.541u 0.242s 0:12.48 70.3% 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 13:40:15 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5597 !!! WARNING: HIR 312 has a net charge of 0.5140 !!! WARNING: HIT 421 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.211150 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): -22.07500 45.20800 ymin,ymax (A): -27.50600 41.79000 zmin,zma (A): 5.942000 78.39300 x,y,z range (A): 67.28300 69.29600 72.45100 scale (grids/A): 2.211150 object centre (A): 11.56650 7.141998 42.16750 number of atom coordinates read : 5597 total number of charged atoms : 5440 net assigned charge : 13.02802 assigned positive charge : 890.8789 centred at (gu) : 94.55937 91.96563 80.56739 assigned negative charge : -877.8596 centred at (gu) : 94.66770 91.83450 80.43236 start vw surface at 0.1500000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 230086 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45340 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 102324 mr = 172070 m= 24242 mr = 81220 m= 2725 mr = 17506 m= 116 mr = 1574 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 9093 time to turn everything in is 1.210000 number of dielectric boundary points 87091 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 43334 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) : 1.474100 object centre at (A) : 11.56650 7.141998 42.16750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1904144E-02 6.7092188E-02 midg,1,midg; midg,igrid,midg -0.5767821 0.2575328 1,midg,midg; igrid,midg,midg 0.2048637 2.9993657E-02 gauss-seidel spectral radius is 0.9991266 estimated iterations to convergence 267 setup time was (sec) 1.490000 now iterating at: 13:40:17 rms-change max change #iterations 10.70812 258.9802 at 10iterations 6.026544 163.2084 at 20iterations 3.371142 71.09692 at 30iterations 1.875786 36.20618 at 40iterations 1.041198 20.93164 at 50iterations 0.5750250 11.14644 at 60iterations 0.3177160 6.383223 at 70iterations 0.1750998 3.608049 at 80iterations 9.6194185E-02 1.818830 at 90iterations 5.2972663E-02 0.9354868 at 100iterations 2.9036066E-02 0.5245361 at 110iterations 1.5969178E-02 0.2802963 at 120iterations 8.7780431E-03 0.1548862 at 130iterations 4.8188120E-03 9.4886780E-02 at 140iterations 2.6514935E-03 5.0373077E-02 at 150iterations 1.4679414E-03 2.4955750E-02 at 160iterations 8.2088471E-04 1.5588760E-02 at 170iterations 4.7078679E-04 9.9105835E-03 at 180iterations finished qdiffx linear iterations at : 13:40:45 total time elapsed so far: 14.44000 # loops : 180 mean,max change (kT/e) : 4.7078679E-04 9.9105835E-03 energy calculations done at 14.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.56000 DelPhi exited at 13:40:45 14.560u 0.297s 0:30.15 49.2% 0+0k 0+0io 0pf+0w