Wed Feb 15 08:56:25 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:56:25 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 ! Automatically converted by prot2crg.py # of charge parameter records: 1065 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3242 !!! WARNING: UMP 529 has a net charge of -2.0000 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: 0.5870809 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): 0.7670001 49.12500 ymin,ymax (A): -7.560000 48.96000 zmin,zma (A): 0.8219999 61.46100 x,y,z range (A): 48.35800 56.52000 60.63900 scale (grids/A): 0.5870809 object centre (A): 24.94600 20.70000 31.14150 number of atom coordinates read : 3242 total number of charged atoms : 3099 net assigned charge : -7.999967 assigned positive charge : 489.4817 centred at (gu) : 89.54828 89.23162 90.79163 assigned negative charge : -497.4830 centred at (gu) : 89.42342 89.13424 90.75637 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7455 nv = 96 ne = 84 npr = 66602 no. pairs analyzed = 66602 no. exposed pairs = 3815 no. arc points = 25997 no. surface atoms = 1314 nbur = 1928 mkacc time = 0.1400000 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 = 1.456000 m= 333 mr = 4273 m= 0 mr = 40 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 3475 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2700 ## 268 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9333 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7460780E-09 -1.2990474E-09 midg,1,midg; midg,igrid,midg -6.2678209E-09 6.5154215E-10 1,midg,midg; igrid,midg,midg -6.7968737E-09 1.4560733E-09 gauss-seidel spectral radius is 0.9850374 estimated iterations to convergence 67 setup time was (sec) 0.5800000 now iterating at: 08:56:26 rms-change max change #iterations 0.1110418 16.28328 at 10iterations 9.0894802E-03 1.297621 at 20iterations 7.7356986E-04 0.1029129 at 30iterations 8.4155894E-05 1.4446259E-02 at 40iterations 1.7894459E-05 2.9468536E-03 at 50iterations finished qdiffx linear iterations at : 08:56:29 total time elapsed so far: 3.030000 # loops : 50 mean,max change (kT/e) : 1.7894459E-05 2.9468536E-03 energy calculations done at 3.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.210000 DelPhi exited at 08:56:29 3.214u 0.150s 0:03.68 91.3% 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 Wed Feb 15 2012 at 08:56:29 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 ! Automatically converted by prot2crg.py # of charge parameter records: 1065 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3242 !!! WARNING: UMP 529 has a net charge of -2.0000 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: 1.761243 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): 0.7670001 49.12500 ymin,ymax (A): -7.560000 48.96000 zmin,zma (A): 0.8219999 61.46100 x,y,z range (A): 48.35800 56.52000 60.63900 scale (grids/A): 1.761243 object centre (A): 24.94600 20.70000 31.14150 number of atom coordinates read : 3242 total number of charged atoms : 3099 net assigned charge : -7.999967 assigned positive charge : 489.4817 centred at (gu) : 88.64416 87.69408 92.37370 assigned negative charge : -497.4830 centred at (gu) : 88.26987 87.40237 92.26873 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 81372 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25997 grid for indexing accessible points = 1.400000 m= 29659 mr = 58473 m= 4046 mr = 22398 m= 139 mr = 2365 m= 0 mr = 26 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 633 time to turn everything in is 0.5700000 number of dielectric boundary points 31954 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 212 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 24117 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) : 0.5870809 object centre at (A) : 24.94600 20.70000 31.14150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4556650E-02 -1.4117007E-02 midg,1,midg; midg,igrid,midg -3.3328377E-02 4.3026757E-04 1,midg,midg; igrid,midg,midg -2.5922321E-02 7.4770916E-03 gauss-seidel spectral radius is 0.9984695 estimated iterations to convergence 203 setup time was (sec) 0.8300000 now iterating at: 08:56:30 rms-change max change #iterations 4.163486 167.6216 at 10iterations 1.856943 57.75706 at 20iterations 0.8332664 27.23584 at 30iterations 0.3735969 11.94912 at 40iterations 0.1679830 5.260752 at 50iterations 7.5330868E-02 2.578917 at 60iterations 3.3895172E-02 1.101734 at 70iterations 1.5147313E-02 0.4853020 at 80iterations 6.8240585E-03 0.2138243 at 90iterations 3.0667309E-03 9.1013908E-02 at 100iterations 1.3760561E-03 5.0460011E-02 at 110iterations 6.2030239E-04 1.9617081E-02 at 120iterations finished qdiffx linear iterations at : 08:56:36 total time elapsed so far: 6.810000 # loops : 120 mean,max change (kT/e) : 6.2030239E-04 1.9617081E-02 energy calculations done at 6.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.980000 DelPhi exited at 08:56:37 6.980u 0.180s 0:07.50 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 Wed Feb 15 2012 at 08:56:37 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 ! Automatically converted by prot2crg.py # of charge parameter records: 1065 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3242 !!! WARNING: UMP 529 has a net charge of -2.0000 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: 2.641864 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): 0.7670001 49.12500 ymin,ymax (A): -7.560000 48.96000 zmin,zma (A): 0.8219999 61.46100 x,y,z range (A): 48.35800 56.52000 60.63900 scale (grids/A): 2.641864 object centre (A): 24.94600 20.70000 31.14150 number of atom coordinates read : 3242 total number of charged atoms : 3099 net assigned charge : -7.999967 assigned positive charge : 489.4817 centred at (gu) : 87.96605 86.54096 93.56046 assigned negative charge : -497.4830 centred at (gu) : 87.40466 86.10333 93.40302 start vw surface at 0.1800000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 188437 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25997 grid for indexing accessible points = 1.400000 m= 98189 mr = 141492 m= 33973 mr = 81584 m= 6984 mr = 27430 m= 694 mr = 5178 m= 20 mr = 387 m= 0 mr = 5 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 2601 time to turn everything in is 1.390000 number of dielectric boundary points 72221 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 24783 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) : 1.761243 object centre at (A) : 24.94600 20.70000 31.14150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3633192 -0.4537480 midg,1,midg; midg,igrid,midg -0.5435277 -1.0414893E-02 1,midg,midg; igrid,midg,midg -0.2920239 0.1149251 gauss-seidel spectral radius is 0.9992217 estimated iterations to convergence 283 setup time was (sec) 1.650000 now iterating at: 08:56:39 rms-change max change #iterations 10.18589 252.0625 at 10iterations 5.880139 155.8798 at 20iterations 3.381822 78.40604 at 30iterations 1.936196 41.21716 at 40iterations 1.106571 20.94352 at 50iterations 0.6301644 11.45549 at 60iterations 0.3588958 6.531033 at 70iterations 0.2042391 3.639179 at 80iterations 0.1160027 2.174675 at 90iterations 6.5920621E-02 1.159882 at 100iterations 3.7333630E-02 0.7161961 at 110iterations 2.1194838E-02 0.4127250 at 120iterations 1.2035056E-02 0.2119713 at 130iterations 6.8072025E-03 0.1194611 at 140iterations 3.8696714E-03 6.6145420E-02 at 150iterations 2.1984978E-03 3.9458275E-02 at 160iterations 1.2470491E-03 2.1239877E-02 at 170iterations 7.1039703E-04 1.3548374E-02 at 180iterations finished qdiffx linear iterations at : 08:56:48 total time elapsed so far: 11.04000 # loops : 180 mean,max change (kT/e) : 7.1039703E-04 1.3548374E-02 energy calculations done at 11.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.21000 DelPhi exited at 08:56:48 11.215u 0.168s 0:11.67 97.4% 0+0k 0+0io 0pf+0w