Tue Oct 11 08:29:46 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 08:29:46 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2895 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6536428 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): -9.993999 37.59600 ymin,ymax (A): -26.84000 22.05800 zmin,zma (A): -9.438000 45.02600 x,y,z range (A): 47.59000 48.89800 54.46400 scale (grids/A): 0.6536428 object centre (A): 13.80100 -2.391000 17.79400 number of atom coordinates read : 2895 total number of charged atoms : 2730 net assigned charge : -1.908978 assigned positive charge : 439.5014 centred at (gu) : 89.37877 90.66309 91.52970 assigned negative charge : -441.4110 centred at (gu) : 89.12774 90.60652 91.47730 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7909 nv = 96 ne = 84 npr = 60453 no. pairs analyzed = 60453 no. exposed pairs = 3432 no. arc points = 23392 no. surface atoms = 1166 nbur = 1729 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 433 mr = 4465 m= 1 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.4000000 number of dielectric boundary points 3828 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2173 ## 200 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 9634 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0127736E-08 8.4587839E-09 midg,1,midg; midg,igrid,midg -1.2824014E-08 7.8632185E-09 1,midg,midg; igrid,midg,midg -6.0541936E-08 3.7288050E-08 gauss-seidel spectral radius is 0.9878856 estimated iterations to convergence 74 setup time was (sec) 0.7300000 now iterating at: 08:29:47 rms-change max change #iterations 0.1725088 26.66166 at 10iterations 1.8251250E-02 2.394341 at 20iterations 1.9698753E-03 0.3148003 at 30iterations 2.6106721E-04 3.4235001E-02 at 40iterations 5.3560037E-05 8.6860657E-03 at 50iterations finished qdiffx linear iterations at : 08:29:50 total time elapsed so far: 4.150000 # loops : 50 mean,max change (kT/e) : 5.3560037E-05 8.6860657E-03 energy calculations done at 4.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.310000 DelPhi exited at 08:29:51 4.310u 0.259s 0:05.08 89.7% 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 08:29:51 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2895 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.960928 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): -9.993999 37.59600 ymin,ymax (A): -26.84000 22.05800 zmin,zma (A): -9.438000 45.02600 x,y,z range (A): 47.59000 48.89800 54.46400 scale (grids/A): 1.960928 object centre (A): 13.80100 -2.391000 17.79400 number of atom coordinates read : 2895 total number of charged atoms : 2730 net assigned charge : -1.908978 assigned positive charge : 439.5014 centred at (gu) : 88.13582 91.98874 94.58830 assigned negative charge : -441.4110 centred at (gu) : 87.38266 91.81892 94.43137 start vw surface at 0.1900000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 84451 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23392 grid for indexing accessible points = 1.400000 m= 31210 mr = 59417 m= 5156 mr = 23078 m= 296 mr = 3230 m= 1 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 3192 time to turn everything in is 0.7800000 number of dielectric boundary points 35298 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 132 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 21540 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) : 0.6536428 object centre at (A) : 13.80100 -2.391000 17.79400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4475766E-02 1.0921692E-03 midg,1,midg; midg,igrid,midg -1.8138848E-02 -2.7316535E-02 1,midg,midg; igrid,midg,midg -1.8240398E-02 5.7587717E-02 gauss-seidel spectral radius is 0.9987285 estimated iterations to convergence 222 setup time was (sec) 1.100000 now iterating at: 08:29:52 rms-change max change #iterations 4.860606 198.4951 at 10iterations 2.346144 84.55595 at 20iterations 1.126239 31.60037 at 30iterations 0.5432495 15.16876 at 40iterations 0.2619995 8.506050 at 50iterations 0.1263343 4.076788 at 60iterations 6.0596202E-02 1.937227 at 70iterations 2.9289642E-02 0.8190765 at 80iterations 1.4120610E-02 0.4295325 at 90iterations 6.8013649E-03 0.1951780 at 100iterations 3.2906623E-03 9.3795776E-02 at 110iterations 1.5984423E-03 4.5179367E-02 at 120iterations finished qdiffx linear iterations at : 08:30:01 total time elapsed so far: 9.700000 # loops : 120 mean,max change (kT/e) : 1.5984423E-03 4.5179367E-02 energy calculations done at 9.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.890000 DelPhi exited at 08:30:01 9.889u 0.274s 0:10.63 95.4% 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 08:30:01 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2895 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.941392 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): -9.993999 37.59600 ymin,ymax (A): -26.84000 22.05800 zmin,zma (A): -9.438000 45.02600 x,y,z range (A): 47.59000 48.89800 54.46400 scale (grids/A): 2.941392 object centre (A): 13.80100 -2.391000 17.79400 number of atom coordinates read : 2895 total number of charged atoms : 2730 net assigned charge : -1.908978 assigned positive charge : 439.5014 centred at (gu) : 87.20341 92.98290 96.88222 assigned negative charge : -441.4110 centred at (gu) : 86.07403 92.72850 96.64693 start vw surface at 0.1500000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 195480 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23392 grid for indexing accessible points = 1.400000 m= 100239 mr = 144255 m= 37217 mr = 82081 m= 9167 mr = 29980 m= 1333 mr = 6736 m= 87 mr = 834 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 10685 time to turn everything in is 1.760000 number of dielectric boundary points 79612 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 21836 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) : 1.960928 object centre at (A) : 13.80100 -2.391000 17.79400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4507825 0.3090066 midg,1,midg; midg,igrid,midg -0.1955608 -0.4247811 1,midg,midg; igrid,midg,midg -3.4723245E-02 0.5466092 gauss-seidel spectral radius is 0.9992829 estimated iterations to convergence 295 setup time was (sec) 2.110000 now iterating at: 08:30:04 rms-change max change #iterations 11.18914 421.9955 at 10iterations 6.607984 155.5714 at 20iterations 3.877671 89.38477 at 30iterations 2.276173 43.64285 at 40iterations 1.332069 23.55559 at 50iterations 0.7775080 14.23892 at 60iterations 0.4545251 7.899944 at 70iterations 0.2644049 4.442499 at 80iterations 0.1540316 3.102448 at 90iterations 8.9675076E-02 1.687418 at 100iterations 5.2230578E-02 0.9113197 at 110iterations 3.0303767E-02 0.4887571 at 120iterations 1.7605666E-02 0.2901373 at 130iterations 1.0267485E-02 0.1717467 at 140iterations 5.9799650E-03 0.1029434 at 150iterations 3.4908939E-03 6.1141968E-02 at 160iterations 2.0460768E-03 3.4181118E-02 at 170iterations 1.2128880E-03 2.2493362E-02 at 180iterations finished qdiffx linear iterations at : 08:30:17 total time elapsed so far: 15.75000 # loops : 180 mean,max change (kT/e) : 1.2128880E-03 2.2493362E-02 energy calculations done at 15.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.93000 DelPhi exited at 08:30:18 15.929u 0.285s 0:16.50 98.1% 0+0k 0+0io 0pf+0w