Tue Oct 11 04:30:02 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 04:30:02 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 = 2750 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6648985 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): -12.58100 37.07800 ymin,ymax (A): -25.99200 22.47600 zmin,zma (A): -8.297000 45.24500 x,y,z range (A): 49.65900 48.46800 53.54200 scale (grids/A): 0.6648985 object centre (A): 12.24850 -1.757999 18.47400 number of atom coordinates read : 2750 total number of charged atoms : 2597 net assigned charge : 1.154017 assigned positive charge : 417.9088 centred at (gu) : 90.48729 90.32651 91.23224 assigned negative charge : -416.7553 centred at (gu) : 90.25086 90.17490 91.13722 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8121 nv = 96 ne = 84 npr = 56846 no. pairs analyzed = 56846 no. exposed pairs = 3342 no. arc points = 23175 no. surface atoms = 1121 nbur = 1629 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 475 mr = 4650 m= 8 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.2000000 number of dielectric boundary points 3899 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2245 ## 201 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 9618 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5702820E-08 3.2830794E-08 midg,1,midg; midg,igrid,midg -3.2045914E-08 4.1310425E-08 1,midg,midg; igrid,midg,midg -5.0147840E-08 6.4434396E-08 gauss-seidel spectral radius is 0.9882842 estimated iterations to convergence 75 setup time was (sec) 0.3900000 now iterating at: 04:30:03 rms-change max change #iterations 0.1837340 25.48932 at 10iterations 2.0142239E-02 2.555630 at 20iterations 2.2232519E-03 0.2879429 at 30iterations 2.5961976E-04 3.1875610E-02 at 40iterations 3.6524383E-05 4.9686432E-03 at 50iterations finished qdiffx linear iterations at : 04:30:06 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 3.6524383E-05 4.9686432E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 04:30:06 3.369u 0.185s 0:04.40 80.4% 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 04:30:07 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 = 2750 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.994696 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): -12.58100 37.07800 ymin,ymax (A): -25.99200 22.47600 zmin,zma (A): -8.297000 45.24500 x,y,z range (A): 49.65900 48.46800 53.54200 scale (grids/A): 1.994696 object centre (A): 12.24850 -1.757999 18.47400 number of atom coordinates read : 2750 total number of charged atoms : 2597 net assigned charge : 1.154017 assigned positive charge : 417.9088 centred at (gu) : 91.46121 90.97892 93.69594 assigned negative charge : -416.7553 centred at (gu) : 90.75256 90.52438 93.41136 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 87102 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23175 grid for indexing accessible points = 1.400000 m= 32801 mr = 61936 m= 5321 mr = 24532 m= 331 mr = 3272 m= 4 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 349 time to turn everything in is 0.4200000 number of dielectric boundary points 35698 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 146 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 20530 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) : 0.6648985 object centre at (A) : 12.24850 -1.757999 18.47400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.3055851E-02 -1.5040868E-03 midg,1,midg; midg,igrid,midg -1.7150700E-02 1.9575393E-02 1,midg,midg; igrid,midg,midg -5.6420607E-03 8.7699264E-02 gauss-seidel spectral radius is 0.9987632 estimated iterations to convergence 225 setup time was (sec) 0.6400000 now iterating at: 04:30:07 rms-change max change #iterations 4.872293 179.9528 at 10iterations 2.371655 74.24039 at 20iterations 1.157329 37.07889 at 30iterations 0.5615093 16.10555 at 40iterations 0.2739682 7.743996 at 50iterations 0.1327252 3.896585 at 60iterations 6.4910054E-02 1.885350 at 70iterations 3.1541452E-02 0.9482479 at 80iterations 1.5379719E-02 0.4423370 at 90iterations 7.4718725E-03 0.2081222 at 100iterations 3.6523708E-03 0.1029282 at 110iterations 1.7899250E-03 4.9606323E-02 at 120iterations finished qdiffx linear iterations at : 04:30:14 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 1.7899250E-03 4.9606323E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 04:30:15 7.871u 0.201s 0:08.51 94.8% 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 Oct 11 2011 at 04:30:15 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 = 2750 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.992043 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): -12.58100 37.07800 ymin,ymax (A): -25.99200 22.47600 zmin,zma (A): -8.297000 45.24500 x,y,z range (A): 49.65900 48.46800 53.54200 scale (grids/A): 2.992043 object centre (A): 12.24850 -1.757999 18.47400 number of atom coordinates read : 2750 total number of charged atoms : 2597 net assigned charge : 1.154017 assigned positive charge : 417.9088 centred at (gu) : 92.19179 91.46824 95.54403 assigned negative charge : -416.7553 centred at (gu) : 91.12873 90.78648 95.11694 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 201518 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23175 grid for indexing accessible points = 1.400000 m= 105527 mr = 149761 m= 38999 mr = 87194 m= 9503 mr = 31569 m= 1442 mr = 7015 m= 119 mr = 962 m= 2 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 1288 time to turn everything in is 1.120000 number of dielectric boundary points 80554 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 20768 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) : 1.994696 object centre at (A) : 12.24850 -1.757999 18.47400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7315960 0.2142779 midg,1,midg; midg,igrid,midg -0.1621971 0.2292629 1,midg,midg; igrid,midg,midg -2.3567284E-02 0.7758391 gauss-seidel spectral radius is 0.9992908 estimated iterations to convergence 296 setup time was (sec) 1.360000 now iterating at: 04:30:17 rms-change max change #iterations 11.16111 440.5421 at 10iterations 6.575381 138.2830 at 20iterations 3.873390 80.38718 at 30iterations 2.274133 47.06819 at 40iterations 1.334563 25.17157 at 50iterations 0.7813454 14.63697 at 60iterations 0.4563375 7.559640 at 70iterations 0.2670285 4.997622 at 80iterations 0.1560449 2.611375 at 90iterations 9.1087840E-02 1.565128 at 100iterations 5.3220339E-02 0.9525566 at 110iterations 3.1077176E-02 0.5261421 at 120iterations 1.8097756E-02 0.2934451 at 130iterations 1.0614337E-02 0.1911850 at 140iterations 6.2023010E-03 0.1138649 at 150iterations 3.6453225E-03 6.4014435E-02 at 160iterations 2.1665017E-03 4.0296555E-02 at 170iterations 1.2982298E-03 2.2645950E-02 at 180iterations finished qdiffx linear iterations at : 04:30:28 total time elapsed so far: 12.79000 # loops : 180 mean,max change (kT/e) : 1.2982298E-03 2.2645950E-02 energy calculations done at 12.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.92000 DelPhi exited at 04:30:29 12.921u 0.218s 0:13.47 97.4% 0+0k 0+0io 0pf+0w