Tue Nov 22 14:18:47 PST 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 Nov 22 2011 at 14:18:52 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5889262 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): -35.42800 10.14200 ymin,ymax (A): 1.086000 42.01900 zmin,zma (A): -2.134000 58.31500 x,y,z range (A): 45.57000 40.93300 60.44900 scale (grids/A): 0.5889262 object centre (A): -12.64300 21.55250 28.09050 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 3.000003 assigned positive charge : 292.9259 centred at (gu) : 90.47327 89.40504 89.77724 assigned negative charge : -289.9262 centred at (gu) : 90.39797 89.53048 89.75620 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4599 nv = 96 ne = 84 npr = 40005 no. pairs analyzed = 40005 no. exposed pairs = 2467 no. arc points = 17560 no. surface atoms = 839 nbur = 1129 mkacc time = 7.0000008E-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 = 1.456000 m= 214 mr = 2485 m= 0 mr = 25 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2303 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1779 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 5687 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.8644228E-10 1.2105253E-09 midg,1,midg; midg,igrid,midg 3.7279957E-09 -1.3669454E-09 1,midg,midg; igrid,midg,midg -5.2437299E-10 2.5710645E-09 gauss-seidel spectral radius is 0.9850324 estimated iterations to convergence 67 setup time was (sec) 0.3700000 now iterating at: 14:18:55 rms-change max change #iterations 8.4383890E-02 16.43840 at 10iterations 6.6513997E-03 1.180542 at 20iterations 5.4002384E-04 0.1099091 at 30iterations 4.3539443E-05 9.5367432E-03 at 40iterations 3.6055790E-06 6.4086914E-04 at 50iterations finished qdiffx linear iterations at : 14:19:05 total time elapsed so far: 3.530000 # loops : 50 mean,max change (kT/e) : 3.6055790E-06 6.4086914E-04 energy calculations done at 3.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.670000 DelPhi exited at 14:19:06 3.674u 0.186s 0:14.90 25.8% 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 Nov 22 2011 at 14:19:09 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.766779 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): -35.42800 10.14200 ymin,ymax (A): 1.086000 42.01900 zmin,zma (A): -2.134000 58.31500 x,y,z range (A): 45.57000 40.93300 60.44900 scale (grids/A): 1.766779 object centre (A): -12.64300 21.55250 28.09050 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 3.000003 assigned positive charge : 292.9259 centred at (gu) : 91.42002 88.21497 89.33172 assigned negative charge : -289.9262 centred at (gu) : 91.19416 88.59147 89.26865 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 49958 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17560 grid for indexing accessible points = 1.400000 m= 17457 mr = 33927 m= 2163 mr = 12909 m= 98 mr = 1284 m= 0 mr = 34 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 21522 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 180 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 14292 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) : 0.5889262 object centre at (A) : -12.64300 21.55250 28.09050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6531510E-02 2.2802345E-02 midg,1,midg; midg,igrid,midg -5.6930723E-05 -8.0084447E-03 1,midg,midg; igrid,midg,midg -8.2004193E-04 -1.0803340E-03 gauss-seidel spectral radius is 0.9983408 estimated iterations to convergence 195 setup time was (sec) 0.5100000 now iterating at: 14:19:13 rms-change max change #iterations 3.136141 147.8424 at 10iterations 1.349515 66.27343 at 20iterations 0.5885911 24.06466 at 30iterations 0.2544062 10.36459 at 40iterations 0.1097148 4.632683 at 50iterations 4.7498856E-02 1.926050 at 60iterations 2.0618776E-02 0.7579737 at 70iterations 8.9599052E-03 0.3541641 at 80iterations 3.8600208E-03 0.1430864 at 90iterations 1.6728316E-03 6.5431595E-02 at 100iterations 7.2688254E-04 3.0364513E-02 at 110iterations 3.1444887E-04 1.1306763E-02 at 120iterations finished qdiffx linear iterations at : 14:19:37 total time elapsed so far: 8.300000 # loops : 120 mean,max change (kT/e) : 3.1444887E-04 1.1306763E-02 energy calculations done at 8.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.440000 DelPhi exited at 14:19:38 8.438u 0.229s 0:29.49 29.3% 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 Tue Nov 22 2011 at 14:19:39 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.650168 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): -35.42800 10.14200 ymin,ymax (A): 1.086000 42.01900 zmin,zma (A): -2.134000 58.31500 x,y,z range (A): 45.57000 40.93300 60.44900 scale (grids/A): 2.650168 object centre (A): -12.64300 21.55250 28.09050 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 3.000003 assigned positive charge : 292.9259 centred at (gu) : 92.13007 87.32236 88.99750 assigned negative charge : -289.9262 centred at (gu) : 91.79120 87.88735 88.90308 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 115681 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17560 grid for indexing accessible points = 1.400000 m= 57383 mr = 82424 m= 19369 mr = 46972 m= 3892 mr = 15574 m= 431 mr = 2859 m= 19 mr = 303 m= 0 mr = 7 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 48636 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 14685 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) : 1.766779 object centre at (A) : -12.64300 21.55250 28.09050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2382468 0.1476937 midg,1,midg; midg,igrid,midg -3.6369566E-02 -0.1086796 1,midg,midg; igrid,midg,midg -2.2480683E-02 -5.2431878E-02 gauss-seidel spectral radius is 0.9991556 estimated iterations to convergence 272 setup time was (sec) 0.9400000 now iterating at: 14:19:45 rms-change max change #iterations 7.605918 280.9561 at 10iterations 4.259731 114.5602 at 20iterations 2.378935 68.31551 at 30iterations 1.321185 30.11288 at 40iterations 0.7314479 16.42630 at 50iterations 0.4064155 9.350365 at 60iterations 0.2240384 5.045734 at 70iterations 0.1237432 2.797370 at 80iterations 6.8546131E-02 1.698050 at 90iterations 3.7827615E-02 0.8139133 at 100iterations 2.0896528E-02 0.4603014 at 110iterations 1.1543060E-02 0.2641735 at 120iterations 6.3764937E-03 0.1493545 at 130iterations 3.5236350E-03 8.3189964E-02 at 140iterations 1.9401783E-03 4.2945385E-02 at 150iterations 1.0722696E-03 2.3803711E-02 at 160iterations 5.9259945E-04 1.3618469E-02 at 170iterations 3.2603089E-04 7.7632070E-03 at 180iterations finished qdiffx linear iterations at : 14:20:20 total time elapsed so far: 12.58000 # loops : 180 mean,max change (kT/e) : 3.2603089E-04 7.7632070E-03 energy calculations done at 12.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.71000 DelPhi exited at 14:20:22 12.710u 0.257s 0:42.80 30.2% 0+0k 0+0io 0pf+0w