Sat Oct 8 17:59:48 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 8 2011 at 17:59:48 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3354 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5379757 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): -49.93500 5.245000 ymin,ymax (A): -125.8480 -59.67400 zmin,zma (A): -16.54300 29.33200 x,y,z range (A): 55.18000 66.17400 45.87500 scale (grids/A): 0.5379757 object centre (A): -22.34500 -92.76100 6.394501 number of atom coordinates read : 3354 total number of charged atoms : 3208 net assigned charge : -4.999993 assigned positive charge : 504.0576 centred at (gu) : 90.17708 90.51025 89.94617 assigned negative charge : -509.0589 centred at (gu) : 90.10559 90.58111 89.94503 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6314 nv = 96 ne = 84 npr = 67449 no. pairs analyzed = 67449 no. exposed pairs = 4253 no. arc points = 29392 no. surface atoms = 1443 nbur = 1911 mkacc time = 0.1500000 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 = 1.624000 m= 250 mr = 3326 m= 0 mr = 7 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3231 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2967 ## 404 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8303 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3439278E-10 -2.1564167E-10 midg,1,midg; midg,igrid,midg 1.4783268E-10 -7.1262096E-10 1,midg,midg; igrid,midg,midg -6.0291439E-10 1.8165899E-10 gauss-seidel spectral radius is 0.9822198 estimated iterations to convergence 62 setup time was (sec) 0.6100000 now iterating at: 17:59:48 rms-change max change #iterations 7.3839739E-02 12.44050 at 10iterations 4.7901822E-03 0.7696023 at 20iterations 4.8657623E-04 8.6233139E-02 at 30iterations 1.1278872E-04 2.4834633E-02 at 40iterations 3.3424418E-05 7.4682236E-03 at 50iterations finished qdiffx linear iterations at : 17:59:52 total time elapsed so far: 4.150000 # loops : 50 mean,max change (kT/e) : 3.3424418E-05 7.4682236E-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) 4.340000 DelPhi exited at 17:59:53 4.341u 0.254s 0:04.88 94.0% 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 Sat Oct 8 2011 at 17:59:53 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3354 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: 1.613927 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): -49.93500 5.245000 ymin,ymax (A): -125.8480 -59.67400 zmin,zma (A): -16.54300 29.33200 x,y,z range (A): 55.18000 66.17400 45.87500 scale (grids/A): 1.613927 object centre (A): -22.34500 -92.76100 6.394501 number of atom coordinates read : 3354 total number of charged atoms : 3208 net assigned charge : -4.999993 assigned positive charge : 504.0576 centred at (gu) : 90.53008 91.53000 89.83784 assigned negative charge : -509.0589 centred at (gu) : 90.31672 91.74260 89.83483 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 70623 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29392 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 22191 mr = 48688 m= 2251 mr = 15377 m= 63 mr = 1052 m= 0 mr = 2 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 513 time to turn everything in is 0.5400000 number of dielectric boundary points 30009 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 367 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 24574 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) : 0.5379757 object centre at (A) : -22.34500 -92.76100 6.394501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.3870717E-03 -1.7700188E-03 midg,1,midg; midg,igrid,midg 1.3676368E-02 1.9139600E-06 1,midg,midg; igrid,midg,midg -8.0569601E-03 3.1692106E-03 gauss-seidel spectral radius is 0.9981782 estimated iterations to convergence 186 setup time was (sec) 0.8600000 now iterating at: 17:59:54 rms-change max change #iterations 3.465148 172.5250 at 10iterations 1.440164 58.76475 at 20iterations 0.5983956 19.59255 at 30iterations 0.2490157 8.802826 at 40iterations 0.1038100 3.908051 at 50iterations 4.3297425E-02 1.598467 at 60iterations 1.8097088E-02 0.6612759 at 70iterations 7.5758942E-03 0.2538710 at 80iterations 3.1804699E-03 0.1079979 at 90iterations 1.3504834E-03 5.0170898E-02 at 100iterations 5.9148448E-04 2.3983002E-02 at 110iterations 2.7215999E-04 1.0137558E-02 at 120iterations finished qdiffx linear iterations at : 18:00:02 total time elapsed so far: 9.380000 # loops : 120 mean,max change (kT/e) : 2.7215999E-04 1.0137558E-02 energy calculations done at 9.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.560000 DelPhi exited at 18:00:03 9.558u 0.291s 0:10.24 96.0% 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 Sat Oct 8 2011 at 18:00:03 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3354 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.420891 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): -49.93500 5.245000 ymin,ymax (A): -125.8480 -59.67400 zmin,zma (A): -16.54300 29.33200 x,y,z range (A): 55.18000 66.17400 45.87500 scale (grids/A): 2.420891 object centre (A): -22.34500 -92.76100 6.394501 number of atom coordinates read : 3354 total number of charged atoms : 3208 net assigned charge : -4.999993 assigned positive charge : 504.0576 centred at (gu) : 90.79504 92.29454 89.75647 assigned negative charge : -509.0589 centred at (gu) : 90.47487 92.61385 89.75212 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 164030 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29392 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 77588 mr = 119219 m= 21747 mr = 61608 m= 3356 mr = 16257 m= 255 mr = 2142 m= 7 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 1665 time to turn everything in is 1.330000 number of dielectric boundary points 67654 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 25624 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) : 1.613927 object centre at (A) : -22.34500 -92.76100 6.394501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.9645264E-02 -2.2614885E-02 midg,1,midg; midg,igrid,midg 0.3807400 0.2545804 1,midg,midg; igrid,midg,midg -0.1103062 7.2819449E-02 gauss-seidel spectral radius is 0.9991426 estimated iterations to convergence 270 setup time was (sec) 1.700000 now iterating at: 18:00:05 rms-change max change #iterations 9.079566 348.8179 at 10iterations 5.101758 144.2913 at 20iterations 2.855920 62.88345 at 30iterations 1.586167 35.05606 at 40iterations 0.8834859 17.89246 at 50iterations 0.4908304 9.834538 at 60iterations 0.2712587 5.697296 at 70iterations 0.1501289 2.783698 at 80iterations 8.2786120E-02 1.699599 at 90iterations 4.5788199E-02 0.8827403 at 100iterations 2.5231494E-02 0.4979410 at 110iterations 1.3928358E-02 0.2645035 at 120iterations 7.6824664E-03 0.1478958 at 130iterations 4.2397240E-03 8.1619263E-02 at 140iterations 2.3454737E-03 4.5436859E-02 at 150iterations 1.2973404E-03 2.7282715E-02 at 160iterations 7.2494370E-04 1.4461517E-02 at 170iterations 4.0921589E-04 8.6460114E-03 at 180iterations finished qdiffx linear iterations at : 18:00:19 total time elapsed so far: 15.92000 # loops : 180 mean,max change (kT/e) : 4.0921589E-04 8.6460114E-03 energy calculations done at 15.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.11000 DelPhi exited at 18:00:20 16.108u 0.343s 0:16.72 98.3% 0+0k 0+0io 0pf+0w