Sat Oct 15 13:51:44 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 Sat Oct 15 2011 at 13:51:44 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2754 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: 0.5300301 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): 45.08600 112.2520 ymin,ymax (A): 21.43900 84.48500 zmin,zma (A): 115.9600 174.2830 x,y,z range (A): 67.16600 63.04600 58.32299 scale (grids/A): 0.5300301 object centre (A): 78.66900 52.96200 145.1215 number of atom coordinates read : 2754 total number of charged atoms : 2557 net assigned charge : -12.49998 assigned positive charge : 411.0823 centred at (gu) : 87.69272 90.75836 90.94373 assigned negative charge : -423.5831 centred at (gu) : 87.70045 90.72672 90.69938 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5121 nv = 96 ne = 84 npr = 52508 no. pairs analyzed = 52508 no. exposed pairs = 3994 no. arc points = 29072 no. surface atoms = 1321 nbur = 1433 mkacc time = 0.1800000 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 = 1.596000 m= 194 mr = 2277 m= 2 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 3032 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2797 ## 407 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 6615 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0012682E-09 5.0330218E-10 midg,1,midg; midg,igrid,midg -4.3320431E-10 -3.7069517E-10 1,midg,midg; igrid,midg,midg -6.9192718E-10 -2.5104760E-10 gauss-seidel spectral radius is 0.9816584 estimated iterations to convergence 61 setup time was (sec) 0.7400000 now iterating at: 13:51:45 rms-change max change #iterations 6.0791288E-02 13.38162 at 10iterations 3.6790248E-03 0.6909180 at 20iterations 2.4577629E-04 4.6997070E-02 at 30iterations 2.7600932E-05 7.6446533E-03 at 40iterations 5.9948898E-06 1.8606186E-03 at 50iterations finished qdiffx linear iterations at : 13:51:49 total time elapsed so far: 4.830000 # loops : 50 mean,max change (kT/e) : 5.9948898E-06 1.8606186E-03 energy calculations done at 4.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.050000 DelPhi exited at 13:51:50 5.055u 0.447s 0:05.93 92.5% 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 15 2011 at 13:51:50 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2754 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: 1.590090 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): 45.08600 112.2520 ymin,ymax (A): 21.43900 84.48500 zmin,zma (A): 115.9600 174.2830 x,y,z range (A): 67.16600 63.04600 58.32299 scale (grids/A): 1.590090 object centre (A): 78.66900 52.96200 145.1215 number of atom coordinates read : 2754 total number of charged atoms : 2557 net assigned charge : -12.49998 assigned positive charge : 411.0823 centred at (gu) : 83.07711 92.27448 92.83061 assigned negative charge : -423.5831 centred at (gu) : 83.10102 92.17963 92.09772 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 56079 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29072 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 15965 mr = 34315 m= 1604 mr = 10383 m= 41 mr = 733 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 28258 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 345 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 19381 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) : 0.5300301 object centre at (A) : 78.66900 52.96200 145.1215 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4258625E-02 1.4023788E-02 midg,1,midg; midg,igrid,midg -1.8434443E-02 -1.2164398E-02 1,midg,midg; igrid,midg,midg -2.5494294E-02 -1.0812948E-02 gauss-seidel spectral radius is 0.9980701 estimated iterations to convergence 181 setup time was (sec) 0.9600000 now iterating at: 13:51:51 rms-change max change #iterations 3.044905 150.9266 at 10iterations 1.223521 54.75113 at 20iterations 0.4917277 19.82932 at 30iterations 0.1989574 9.005907 at 40iterations 8.0439553E-02 3.393446 at 50iterations 3.2526709E-02 1.254147 at 60iterations 1.3158596E-02 0.5309448 at 70iterations 5.3219497E-03 0.1932812 at 80iterations 2.1561501E-03 8.8394165E-02 at 90iterations 8.7309798E-04 3.3603430E-02 at 100iterations 3.5513728E-04 1.4841080E-02 at 110iterations 1.4430066E-04 7.3623657E-03 at 120iterations finished qdiffx linear iterations at : 13:52:01 total time elapsed so far: 11.04000 # loops : 120 mean,max change (kT/e) : 1.4430066E-04 7.3623657E-03 energy calculations done at 11.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.27000 DelPhi exited at 13:52:02 11.271u 0.514s 0:12.33 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 15 2011 at 13:52:02 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2754 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: 2.385135 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): 45.08600 112.2520 ymin,ymax (A): 21.43900 84.48500 zmin,zma (A): 115.9600 174.2830 x,y,z range (A): 67.16600 63.04600 58.32299 scale (grids/A): 2.385135 object centre (A): 78.66900 52.96200 145.1215 number of atom coordinates read : 2754 total number of charged atoms : 2557 net assigned charge : -12.49998 assigned positive charge : 411.0823 centred at (gu) : 79.61549 93.41161 94.24574 assigned negative charge : -423.5831 centred at (gu) : 79.65144 93.26942 93.14657 start vw surface at 0.1700000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 129800 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29072 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 55450 mr = 84919 m= 15507 mr = 41772 m= 2493 mr = 11340 m= 152 mr = 1558 m= 3 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.490000 number of dielectric boundary points 63788 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 20417 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) : 1.590090 object centre at (A) : 78.66900 52.96200 145.1215 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2281998 0.2238572 midg,1,midg; midg,igrid,midg -0.3338255 -0.1063305 1,midg,midg; igrid,midg,midg -0.3847278 -0.1079818 gauss-seidel spectral radius is 0.9990952 estimated iterations to convergence 263 setup time was (sec) 1.900000 now iterating at: 13:52:05 rms-change max change #iterations 8.087761 330.6996 at 10iterations 4.492785 125.3263 at 20iterations 2.471151 76.75565 at 30iterations 1.356470 34.02674 at 40iterations 0.7383216 21.70129 at 50iterations 0.4024739 9.172585 at 60iterations 0.2188604 5.139015 at 70iterations 0.1184523 2.827951 at 80iterations 6.4253218E-02 1.433075 at 90iterations 3.4835998E-02 0.7285235 at 100iterations 1.8859431E-02 0.4399261 at 110iterations 1.0215797E-02 0.2321510 at 120iterations 5.5146413E-03 0.1207504 at 130iterations 2.9787880E-03 6.9396973E-02 at 140iterations 1.6117777E-03 3.5465240E-02 at 150iterations 8.7307661E-04 1.9668579E-02 at 160iterations 4.7164009E-04 1.0475159E-02 at 170iterations 2.5475567E-04 5.7678223E-03 at 180iterations finished qdiffx linear iterations at : 13:52:30 total time elapsed so far: 26.74000 # loops : 180 mean,max change (kT/e) : 2.5475567E-04 5.7678223E-03 energy calculations done at 26.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 26.95000 DelPhi exited at 13:52:31 26.954u 0.563s 0:28.28 97.2% 0+0k 0+0io 0pf+0w