Mon Oct 10 14:25:44 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 Mon Oct 10 2011 at 14:25:44 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2298 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: 0.6063393 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): -23.68700 22.52400 ymin,ymax (A): -23.99000 34.72300 zmin,zma (A): -37.12700 15.63600 x,y,z range (A): 46.21100 58.71300 52.76300 scale (grids/A): 0.6063393 object centre (A): -0.5815001 5.366500 -10.74550 number of atom coordinates read : 2298 total number of charged atoms : 2144 net assigned charge : 2.000002 assigned positive charge : 335.2763 centred at (gu) : 89.20793 89.79285 89.94390 assigned negative charge : -333.2767 centred at (gu) : 89.14440 89.63941 89.89141 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 5750 nv = 96 ne = 84 npr = 45711 no. pairs analyzed = 45711 no. exposed pairs = 3200 no. arc points = 22230 no. surface atoms = 1070 nbur = 1228 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 273 mr = 2829 m= 0 mr = 16 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3178 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2238 ## 227 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 6986 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.2823327E-10 3.0401583E-09 midg,1,midg; midg,igrid,midg -5.0876103E-09 6.5168435E-09 1,midg,midg; igrid,midg,midg -1.6218172E-09 2.9243101E-09 gauss-seidel spectral radius is 0.9859030 estimated iterations to convergence 69 setup time was (sec) 0.6700000 now iterating at: 14:25:45 rms-change max change #iterations 0.1024788 15.79037 at 10iterations 8.7790694E-03 1.427067 at 20iterations 7.6458341E-04 0.1257267 at 30iterations 6.5923537E-05 1.1425018E-02 at 40iterations 5.9033573E-06 1.1205673E-03 at 50iterations finished qdiffx linear iterations at : 14:25:48 total time elapsed so far: 4.010000 # loops : 50 mean,max change (kT/e) : 5.9033573E-06 1.1205673E-03 energy calculations done at 4.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 14:25:49 4.243u 0.225s 0:05.23 85.2% 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 14:25:49 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2298 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: 1.819018 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): -23.68700 22.52400 ymin,ymax (A): -23.99000 34.72300 zmin,zma (A): -37.12700 15.63600 x,y,z range (A): 46.21100 58.71300 52.76300 scale (grids/A): 1.819018 object centre (A): -0.5815001 5.366500 -10.74550 number of atom coordinates read : 2298 total number of charged atoms : 2144 net assigned charge : 2.000002 assigned positive charge : 335.2763 centred at (gu) : 87.62350 89.37819 89.83133 assigned negative charge : -333.2767 centred at (gu) : 87.43302 88.91809 89.67410 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 62162 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22230 grid for indexing accessible points = 1.400000 m= 20783 mr = 40738 m= 2722 mr = 14324 m= 117 mr = 1336 m= 3 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 29371 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 171 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 16758 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) : 0.6063393 object centre at (A) : -0.5815001 5.366500 -10.74550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2980154E-03 6.6752047E-03 midg,1,midg; midg,igrid,midg 4.4287951E-03 4.3584029E-03 1,midg,midg; igrid,midg,midg 1.3663463E-03 3.4655402E-03 gauss-seidel spectral radius is 0.9984866 estimated iterations to convergence 204 setup time was (sec) 0.9800000 now iterating at: 14:25:50 rms-change max change #iterations 3.557342 198.3089 at 10iterations 1.584746 59.62382 at 20iterations 0.7121865 25.43980 at 30iterations 0.3191174 12.87319 at 40iterations 0.1427844 5.002067 at 50iterations 6.4399026E-02 2.506622 at 60iterations 2.8889375E-02 1.144314 at 70iterations 1.2961233E-02 0.4614639 at 80iterations 5.8217663E-03 0.2161463 at 90iterations 2.6191692E-03 9.7519577E-02 at 100iterations 1.1753879E-03 4.3544769E-02 at 110iterations 5.2900770E-04 1.8582344E-02 at 120iterations finished qdiffx linear iterations at : 14:25:58 total time elapsed so far: 8.720000 # loops : 120 mean,max change (kT/e) : 5.2900770E-04 1.8582344E-02 energy calculations done at 8.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.970000 DelPhi exited at 14:25:59 8.973u 0.250s 0:09.90 93.1% 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 14:25:59 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2298 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: 2.728527 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): -23.68700 22.52400 ymin,ymax (A): -23.99000 34.72300 zmin,zma (A): -37.12700 15.63600 x,y,z range (A): 46.21100 58.71300 52.76300 scale (grids/A): 2.728527 object centre (A): -0.5815001 5.366500 -10.74550 number of atom coordinates read : 2298 total number of charged atoms : 2144 net assigned charge : 2.000002 assigned positive charge : 335.2763 centred at (gu) : 86.43501 89.06725 89.74707 assigned negative charge : -333.2767 centred at (gu) : 86.14948 88.37711 89.51108 start vw surface at 0.1900000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 143861 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22230 grid for indexing accessible points = 1.400000 m= 68878 mr = 99866 m= 22513 mr = 54157 m= 4454 mr = 16964 m= 444 mr = 2810 m= 20 mr = 204 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.470000 number of dielectric boundary points 66166 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 17150 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) : 1.819018 object centre at (A) : -0.5815001 5.366500 -10.74550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1533169 7.8346685E-02 midg,1,midg; midg,igrid,midg 0.1639050 -9.2978828E-02 1,midg,midg; igrid,midg,midg 4.2142596E-02 1.3479573E-02 gauss-seidel spectral radius is 0.9992217 estimated iterations to convergence 283 setup time was (sec) 1.860000 now iterating at: 14:26:01 rms-change max change #iterations 8.758063 295.8275 at 10iterations 5.108356 134.1478 at 20iterations 2.956269 74.92831 at 30iterations 1.703453 39.35969 at 40iterations 0.9760665 24.31756 at 50iterations 0.5574962 13.35323 at 60iterations 0.3185163 10.10960 at 70iterations 0.1808083 3.759078 at 80iterations 0.1029210 2.138292 at 90iterations 5.8536902E-02 1.319341 at 100iterations 3.3299491E-02 0.6786528 at 110iterations 1.8838311E-02 0.3925329 at 120iterations 1.0698822E-02 0.2465363 at 130iterations 6.0599502E-03 0.1220922 at 140iterations 3.4343721E-03 7.1436882E-02 at 150iterations 1.9461270E-03 3.9022446E-02 at 160iterations 1.1009834E-03 2.4204254E-02 at 170iterations 6.2321499E-04 1.3768196E-02 at 180iterations finished qdiffx linear iterations at : 14:26:14 total time elapsed so far: 14.80000 # loops : 180 mean,max change (kT/e) : 6.2321499E-04 1.3768196E-02 energy calculations done at 14.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.03000 DelPhi exited at 14:26:15 15.028u 0.215s 0:15.82 96.2% 0+0k 0+0io 0pf+0w