Sat Oct 15 11:54:21 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 15 2011 at 11:54:21 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3300 !!! WARNING: HIT 82 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 0.5742399 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): -16.29000 40.06800 ymin,ymax (A): 16.75400 76.39100 zmin,zma (A): 25.04800 87.04300 x,y,z range (A): 56.35800 59.63700 61.99500 scale (grids/A): 0.5742399 object centre (A): 11.88900 46.57250 56.04550 number of atom coordinates read : 3300 total number of charged atoms : 3159 net assigned charge : 13.74002 assigned positive charge : 488.6677 centred at (gu) : 89.92321 90.01526 91.00121 assigned negative charge : -474.9294 centred at (gu) : 89.80128 90.03608 91.17926 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7367 nv = 96 ne = 84 npr = 65230 no. pairs analyzed = 65230 no. exposed pairs = 4366 no. arc points = 31952 no. surface atoms = 1451 nbur = 1849 mkacc time = 0.1700000 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 = 1.484000 m= 321 mr = 3705 m= 0 mr = 24 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.3900000 number of dielectric boundary points 3959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3171 ## 332 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9327 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6465551E-09 -1.3487000E-09 midg,1,midg; midg,igrid,midg 2.8890421E-09 2.0995825E-09 1,midg,midg; igrid,midg,midg 9.8704336E-11 4.7390016E-09 gauss-seidel spectral radius is 0.9843897 estimated iterations to convergence 66 setup time was (sec) 0.7000000 now iterating at: 11:54:23 rms-change max change #iterations 9.9718444E-02 15.83074 at 10iterations 7.4421978E-03 1.193672 at 20iterations 5.8993470E-04 8.4973812E-02 at 30iterations 5.4461329E-05 7.6885223E-03 at 40iterations 7.1556888E-06 7.5531006E-04 at 50iterations finished qdiffx linear iterations at : 11:54:27 total time elapsed so far: 5.250000 # loops : 50 mean,max change (kT/e) : 7.1556888E-06 7.5531006E-04 energy calculations done at 5.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.420000 DelPhi exited at 11:54:28 5.428u 0.462s 0:06.17 95.2% 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 Sat Oct 15 2011 at 11:54:28 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3300 !!! WARNING: HIT 82 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 1.722720 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): -16.29000 40.06800 ymin,ymax (A): 16.75400 76.39100 zmin,zma (A): 25.04800 87.04300 x,y,z range (A): 56.35800 59.63700 61.99500 scale (grids/A): 1.722720 object centre (A): 11.88900 46.57250 56.04550 number of atom coordinates read : 3300 total number of charged atoms : 3159 net assigned charge : 13.74002 assigned positive charge : 488.6677 centred at (gu) : 89.76873 90.04473 93.00252 assigned negative charge : -474.9294 centred at (gu) : 89.40349 90.10791 93.53757 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 80089 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31952 grid for indexing accessible points = 1.400000 m= 25907 mr = 53006 m= 3236 mr = 17928 m= 117 mr = 1736 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 1568 time to turn everything in is 0.6900000 number of dielectric boundary points 36663 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 310 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 24562 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) : 0.5742399 object centre at (A) : 11.88900 46.57250 56.04550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6732113E-02 1.2340557E-02 midg,1,midg; midg,igrid,midg 3.5501052E-02 1.8884655E-02 1,midg,midg; igrid,midg,midg -6.2546441E-03 1.6938830E-02 gauss-seidel spectral radius is 0.9984249 estimated iterations to convergence 200 setup time was (sec) 1.060000 now iterating at: 11:54:29 rms-change max change #iterations 3.945918 167.6409 at 10iterations 1.733206 56.09013 at 20iterations 0.7644790 26.80798 at 30iterations 0.3377347 10.77034 at 40iterations 0.1490195 4.725098 at 50iterations 6.5531433E-02 2.180946 at 60iterations 2.9176811E-02 0.9593964 at 70iterations 1.2880160E-02 0.4249430 at 80iterations 5.6954627E-03 0.1800556 at 90iterations 2.5235787E-03 7.7127457E-02 at 100iterations 1.1137043E-03 3.5840988E-02 at 110iterations 4.9482583E-04 1.5314102E-02 at 120iterations finished qdiffx linear iterations at : 11:54:41 total time elapsed so far: 13.14000 # loops : 120 mean,max change (kT/e) : 4.9482583E-04 1.5314102E-02 energy calculations done at 13.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.32000 DelPhi exited at 11:54:42 13.322u 0.520s 0:14.18 97.6% 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 15 2011 at 11:54:42 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3300 !!! WARNING: HIT 82 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 2.584080 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): -16.29000 40.06800 ymin,ymax (A): 16.75400 76.39100 zmin,zma (A): 25.04800 87.04300 x,y,z range (A): 56.35800 59.63700 61.99500 scale (grids/A): 2.584080 object centre (A): 11.88900 46.57250 56.04550 number of atom coordinates read : 3300 total number of charged atoms : 3159 net assigned charge : 13.74002 assigned positive charge : 488.6677 centred at (gu) : 89.65289 90.06700 94.50352 assigned negative charge : -474.9294 centred at (gu) : 89.10513 90.16179 95.30633 start vw surface at 0.1400000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 186102 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31952 grid for indexing accessible points = 1.400000 m= 86848 mr = 130241 m= 27427 mr = 68403 m= 5300 mr = 20910 m= 473 mr = 3621 m= 13 mr = 242 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 5084 time to turn everything in is 1.710000 number of dielectric boundary points 82747 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 25247 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) : 1.722720 object centre at (A) : 11.88900 46.57250 56.04550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7100739 0.1320859 midg,1,midg; midg,igrid,midg 0.5485530 0.3456680 1,midg,midg; igrid,midg,midg -4.2280927E-02 0.2275039 gauss-seidel spectral radius is 0.9992262 estimated iterations to convergence 284 setup time was (sec) 2.120000 now iterating at: 11:54:45 rms-change max change #iterations 9.862189 322.0345 at 10iterations 5.747447 146.0174 at 20iterations 3.320641 83.49363 at 30iterations 1.915376 42.22387 at 40iterations 1.097029 22.23355 at 50iterations 0.6283791 13.25663 at 60iterations 0.3574669 7.370941 at 70iterations 0.2040945 3.692886 at 80iterations 0.1160079 2.359566 at 90iterations 6.6043869E-02 1.186566 at 100iterations 3.7497167E-02 0.6905929 at 110iterations 2.1304011E-02 0.4174910 at 120iterations 1.2097505E-02 0.2267532 at 130iterations 6.8548298E-03 0.1218224 at 140iterations 3.8905081E-03 7.2525024E-02 at 150iterations 2.2088597E-03 4.4219971E-02 at 160iterations 1.2530067E-03 2.3132324E-02 at 170iterations 7.1041333E-04 1.2774467E-02 at 180iterations finished qdiffx linear iterations at : 11:55:04 total time elapsed so far: 22.01000 # loops : 180 mean,max change (kT/e) : 7.1041333E-04 1.2774467E-02 energy calculations done at 22.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.17000 DelPhi exited at 11:55:05 22.177u 0.562s 0:23.00 98.8% 0+0k 0+0io 0pf+0w