Sat Oct 8 23:10:53 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 23:10:53 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2424 !!! WARNING: HIT 84 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6440175 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): -13.23200 39.20200 ymin,ymax (A): 10.12800 65.40600 zmin,zma (A): -9.588000 33.45200 x,y,z range (A): 52.43400 55.27800 43.04000 scale (grids/A): 0.6440175 object centre (A): 12.98500 37.76700 11.93200 number of atom coordinates read : 2424 total number of charged atoms : 2289 net assigned charge : 11.51402 assigned positive charge : 355.5142 centred at (gu) : 90.50145 89.17557 90.86471 assigned negative charge : -344.0010 centred at (gu) : 90.51744 89.21220 90.79363 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6837 nv = 96 ne = 84 npr = 48561 no. pairs analyzed = 48561 no. exposed pairs = 3197 no. arc points = 22789 no. surface atoms = 1083 nbur = 1341 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 415 mr = 3505 m= 1 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3699 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2221 ## 180 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8112 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.8042498E-09 3.2119679E-08 midg,1,midg; midg,igrid,midg 2.7156453E-08 1.2230350E-08 1,midg,midg; igrid,midg,midg 1.8496172E-08 1.8639193E-08 gauss-seidel spectral radius is 0.9875001 estimated iterations to convergence 73 setup time was (sec) 0.3800000 now iterating at: 23:10:53 rms-change max change #iterations 0.1403730 24.19903 at 10iterations 1.4017176E-02 2.085785 at 20iterations 1.6334475E-03 0.2098389 at 30iterations 3.4355969E-04 5.1200867E-02 at 40iterations 1.0995640E-04 1.8193245E-02 at 50iterations finished qdiffx linear iterations at : 23:10:56 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 1.0995640E-04 1.8193245E-02 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 23:10:56 3.364u 0.181s 0:03.86 91.7% 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 Sat Oct 8 2011 at 23:10:56 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2424 !!! WARNING: HIT 84 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.932052 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): -13.23200 39.20200 ymin,ymax (A): 10.12800 65.40600 zmin,zma (A): -9.588000 33.45200 x,y,z range (A): 52.43400 55.27800 43.04000 scale (grids/A): 1.932052 object centre (A): 12.98500 37.76700 11.93200 number of atom coordinates read : 2424 total number of charged atoms : 2289 net assigned charge : 11.51402 assigned positive charge : 355.5142 centred at (gu) : 91.50417 87.52628 92.59381 assigned negative charge : -344.0010 centred at (gu) : 91.55235 87.63683 92.38099 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 73003 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22789 grid for indexing accessible points = 1.400000 m= 26950 mr = 48780 m= 4863 mr = 19206 m= 349 mr = 2975 m= 4 mr = 118 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 34090 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 18025 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) : 0.6440175 object centre at (A) : 12.98500 37.76700 11.93200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3718080E-03 3.1954765E-02 midg,1,midg; midg,igrid,midg 4.0970422E-02 5.1168539E-02 1,midg,midg; igrid,midg,midg 4.7272887E-02 5.0671339E-02 gauss-seidel spectral radius is 0.9986659 estimated iterations to convergence 217 setup time was (sec) 0.5800000 now iterating at: 23:10:57 rms-change max change #iterations 4.136682 175.8414 at 10iterations 1.947533 70.85795 at 20iterations 0.9194905 27.66170 at 30iterations 0.4329899 15.93294 at 40iterations 0.2051691 7.135085 at 50iterations 9.6462585E-02 3.228336 at 60iterations 4.5781821E-02 1.420274 at 70iterations 2.1579443E-02 0.6542478 at 80iterations 1.0248189E-02 0.3097076 at 90iterations 4.9278787E-03 0.1520176 at 100iterations 2.4118233E-03 7.8969955E-02 at 110iterations 1.2257803E-03 4.0845871E-02 at 120iterations finished qdiffx linear iterations at : 23:11:04 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 1.2257803E-03 4.0845871E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 23:11:05 7.787u 0.209s 0:08.35 95.5% 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 23:11:05 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2424 !!! WARNING: HIT 84 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.898079 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): -13.23200 39.20200 ymin,ymax (A): 10.12800 65.40600 zmin,zma (A): -9.588000 33.45200 x,y,z range (A): 52.43400 55.27800 43.04000 scale (grids/A): 2.898079 object centre (A): 12.98500 37.76700 11.93200 number of atom coordinates read : 2424 total number of charged atoms : 2289 net assigned charge : 11.51402 assigned positive charge : 355.5142 centred at (gu) : 92.25614 86.28932 93.89066 assigned negative charge : -344.0010 centred at (gu) : 92.32854 86.45535 93.57149 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 168636 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22789 grid for indexing accessible points = 1.400000 m= 84604 mr = 118682 m= 32980 mr = 67545 m= 8701 mr = 26014 m= 1442 mr = 6367 m= 99 mr = 943 m= 0 mr = 37 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9400000 number of dielectric boundary points 76874 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 18304 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) : 1.932052 object centre at (A) : 12.98500 37.76700 11.93200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7187269E-02 0.2998711 midg,1,midg; midg,igrid,midg 0.4294341 0.7918864 1,midg,midg; igrid,midg,midg 0.5100285 0.4529663 gauss-seidel spectral radius is 0.9992741 estimated iterations to convergence 293 setup time was (sec) 1.190000 now iterating at: 23:11:06 rms-change max change #iterations 9.767906 434.1608 at 10iterations 5.812608 163.0165 at 20iterations 3.425591 74.42734 at 30iterations 2.015569 43.76526 at 40iterations 1.177772 25.84558 at 50iterations 0.6885886 16.82893 at 60iterations 0.4019638 9.404458 at 70iterations 0.2340167 5.286674 at 80iterations 0.1359046 2.500680 at 90iterations 7.9123318E-02 1.518612 at 100iterations 4.5900617E-02 0.8735161 at 110iterations 2.6708638E-02 0.5477772 at 120iterations 1.5517354E-02 0.3043232 at 130iterations 9.0655219E-03 0.1989954 at 140iterations 5.3218682E-03 0.1022415 at 150iterations 3.1809807E-03 6.3446045E-02 at 160iterations 1.9519158E-03 4.0077209E-02 at 170iterations 1.2511525E-03 2.6517868E-02 at 180iterations finished qdiffx linear iterations at : 23:11:18 total time elapsed so far: 12.59000 # loops : 180 mean,max change (kT/e) : 1.2511525E-03 2.6517868E-02 energy calculations done at 12.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.73000 DelPhi exited at 23:11:18 12.729u 0.204s 0:13.22 97.7% 0+0k 0+0io 0pf+0w