Tue Oct 11 03:25:22 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 03:25:22 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2532 !!! WARNING: HIT 283 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: 0.5715386 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): -14.62700 38.81700 ymin,ymax (A): -24.28100 38.00700 zmin,zma (A): -15.23900 34.52000 x,y,z range (A): 53.44400 62.28800 49.75900 scale (grids/A): 0.5715386 object centre (A): 12.09500 6.863000 9.640499 number of atom coordinates read : 2532 total number of charged atoms : 2388 net assigned charge : 7.514025 assigned positive charge : 385.2450 centred at (gu) : 87.90627 88.70914 90.21061 assigned negative charge : -377.7317 centred at (gu) : 87.85101 88.75024 90.20081 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5300 nv = 96 ne = 84 npr = 51146 no. pairs analyzed = 51146 no. exposed pairs = 3295 no. arc points = 23007 no. surface atoms = 1100 nbur = 1432 mkacc time = 9.0000004E-02 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 = 1.512000 m= 247 mr = 2658 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.1900000 number of dielectric boundary points 2866 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2329 ## 252 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 6878 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0314398E-09 1.4235894E-09 midg,1,midg; midg,igrid,midg 2.4262854E-09 4.8483811E-10 1,midg,midg; igrid,midg,midg 6.8728401E-10 1.2232831E-09 gauss-seidel spectral radius is 0.9841661 estimated iterations to convergence 65 setup time was (sec) 0.3800000 now iterating at: 03:25:23 rms-change max change #iterations 8.7580435E-02 14.66377 at 10iterations 6.4635645E-03 1.009968 at 20iterations 4.9005507E-04 8.1754684E-02 at 30iterations 4.0898623E-05 6.8473816E-03 at 40iterations 4.7353060E-06 9.2220306E-04 at 50iterations finished qdiffx linear iterations at : 03:25:25 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 4.7353060E-06 9.2220306E-04 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 03:25:26 3.385u 0.154s 0:04.01 88.0% 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 Tue Oct 11 2011 at 03:25:26 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2532 !!! WARNING: HIT 283 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: 1.714616 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): -14.62700 38.81700 ymin,ymax (A): -24.28100 38.00700 zmin,zma (A): -15.23900 34.52000 x,y,z range (A): 53.44400 62.28800 49.75900 scale (grids/A): 1.714616 object centre (A): 12.09500 6.863000 9.640499 number of atom coordinates read : 2532 total number of charged atoms : 2388 net assigned charge : 7.514025 assigned positive charge : 385.2450 centred at (gu) : 83.71844 86.12697 90.63120 assigned negative charge : -377.7317 centred at (gu) : 83.55295 86.25055 90.60215 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 58119 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23007 grid for indexing accessible points = 1.400000 m= 18600 mr = 38575 m= 2303 mr = 12772 m= 86 mr = 1215 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 405 time to turn everything in is 0.2900000 number of dielectric boundary points 26537 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 236 iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 18425 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) : 0.5715386 object centre at (A) : 12.09500 6.863000 9.640499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0091242E-03 9.3086865E-03 midg,1,midg; midg,igrid,midg 8.7885149E-03 -9.8520843E-03 1,midg,midg; igrid,midg,midg 8.2887057E-03 -4.5663308E-04 gauss-seidel spectral radius is 0.9983090 estimated iterations to convergence 193 setup time was (sec) 0.5000000 now iterating at: 03:25:27 rms-change max change #iterations 3.407992 148.5972 at 10iterations 1.456446 59.08344 at 20iterations 0.6262184 26.22902 at 30iterations 0.2691903 10.78961 at 40iterations 0.1155263 4.638420 at 50iterations 4.9458575E-02 2.025374 at 60iterations 2.1292018E-02 0.7930107 at 70iterations 9.1739139E-03 0.3625345 at 80iterations 3.9302073E-03 0.1378174 at 90iterations 1.6930124E-03 6.4863205E-02 at 100iterations 7.2707701E-04 2.8176308E-02 at 110iterations 3.1283119E-04 1.3197899E-02 at 120iterations finished qdiffx linear iterations at : 03:25:34 total time elapsed so far: 7.470000 # loops : 120 mean,max change (kT/e) : 3.1283119E-04 1.3197899E-02 energy calculations done at 7.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.590000 DelPhi exited at 03:25:34 7.597u 0.203s 0:08.19 95.1% 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 Tue Oct 11 2011 at 03:25:34 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2532 !!! WARNING: HIT 283 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: 2.571924 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): -14.62700 38.81700 ymin,ymax (A): -24.28100 38.00700 zmin,zma (A): -15.23900 34.52000 x,y,z range (A): 53.44400 62.28800 49.75900 scale (grids/A): 2.571924 object centre (A): 12.09500 6.863000 9.640499 number of atom coordinates read : 2532 total number of charged atoms : 2388 net assigned charge : 7.514025 assigned positive charge : 385.2450 centred at (gu) : 80.57747 84.19021 90.94659 assigned negative charge : -377.7317 centred at (gu) : 80.32938 84.37583 90.90325 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 134865 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23007 grid for indexing accessible points = 1.400000 m= 62519 mr = 94520 m= 19627 mr = 48974 m= 3959 mr = 14987 m= 337 mr = 2754 m= 11 mr = 149 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 1293 time to turn everything in is 0.7200000 number of dielectric boundary points 59934 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 19092 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) : 1.714616 object centre at (A) : 12.09500 6.863000 9.640499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6795240E-03 0.1039502 midg,1,midg; midg,igrid,midg 9.4937637E-02 -0.2614623 1,midg,midg; igrid,midg,midg 9.9513546E-02 -5.1164884E-02 gauss-seidel spectral radius is 0.9991669 estimated iterations to convergence 274 setup time was (sec) 0.9500000 now iterating at: 03:25:35 rms-change max change #iterations 8.585793 306.3021 at 10iterations 4.886866 123.7559 at 20iterations 2.767529 73.02670 at 30iterations 1.559271 34.44965 at 40iterations 0.8737510 19.66465 at 50iterations 0.4884939 12.60716 at 60iterations 0.2732559 6.566870 at 70iterations 0.1526448 3.479826 at 80iterations 8.5032560E-02 1.854603 at 90iterations 4.7349487E-02 1.076717 at 100iterations 2.6352894E-02 0.6424456 at 110iterations 1.4636663E-02 0.3105698 at 120iterations 8.1471531E-03 0.1696353 at 130iterations 4.5286315E-03 9.8758698E-02 at 140iterations 2.5080766E-03 5.4092407E-02 at 150iterations 1.3946084E-03 3.0288696E-02 at 160iterations 7.7583326E-04 1.6515732E-02 at 170iterations 4.3083698E-04 1.0732651E-02 at 180iterations finished qdiffx linear iterations at : 03:25:46 total time elapsed so far: 11.88000 # loops : 180 mean,max change (kT/e) : 4.3083698E-04 1.0732651E-02 energy calculations done at 11.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.00000 DelPhi exited at 03:25:47 12.006u 0.213s 0:12.92 94.5% 0+0k 0+0io 0pf+0w