Tue Oct 11 06:33:31 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+sph.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 = amb.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 06:33:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7223733 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): -40.77900 -1.429000 ymin,ymax (A): -27.10500 17.66700 zmin,zma (A): -14.90600 34.37600 x,y,z range (A): 39.35000 44.77200 49.28200 scale (grids/A): 0.7223733 object centre (A): -21.10400 -4.719000 9.735000 number of atom coordinates read : 2089 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 91.44940 90.18865 88.97048 assigned negative charge : -311.0742 centred at (gu) : 91.48934 90.32077 88.89700 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7388 nv = 96 ne = 84 npr = 42229 no. pairs analyzed = 42229 no. exposed pairs = 2521 no. arc points = 17094 no. surface atoms = 854 nbur = 1235 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 488 mr = 4288 m= 5 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 9.9999979E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3517 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1562 ## 115 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8078 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3352947E-08 1.0572469E-07 midg,1,midg; midg,igrid,midg 1.6149124E-07 -1.3220273E-08 1,midg,midg; igrid,midg,midg 8.0730139E-08 6.6519405E-08 gauss-seidel spectral radius is 0.9900063 estimated iterations to convergence 81 setup time was (sec) 0.5000000 now iterating at: 06:33:31 rms-change max change #iterations 0.2125982 27.34912 at 10iterations 2.7999485E-02 3.598299 at 20iterations 3.8311374E-03 0.5186300 at 30iterations 5.9497164E-04 8.1521988E-02 at 40iterations 1.3098262E-04 1.5609741E-02 at 50iterations finished qdiffx linear iterations at : 06:33:34 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 1.3098262E-04 1.5609741E-02 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.060000 DelPhi exited at 06:33:34 3.067u 0.117s 0:03.57 88.7% 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 06:33:34 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.167120 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): -40.77900 -1.429000 ymin,ymax (A): -27.10500 17.66700 zmin,zma (A): -14.90600 34.37600 x,y,z range (A): 39.35000 44.77200 49.28200 scale (grids/A): 2.167120 object centre (A): -21.10400 -4.719000 9.735000 number of atom coordinates read : 2089 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 94.34815 90.56605 86.91143 assigned negative charge : -311.0742 centred at (gu) : 94.46815 90.96236 86.69112 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 78141 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17094 grid for indexing accessible points = 1.400000 m= 31844 mr = 55849 m= 6553 mr = 24473 m= 625 mr = 4409 m= 19 mr = 359 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 32092 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 41 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 15567 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) : 0.7223733 object centre at (A) : -21.10400 -4.719000 9.735000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1746497E-02 4.4635065E-02 midg,1,midg; midg,igrid,midg 4.5904715E-02 4.7900178E-03 1,midg,midg; igrid,midg,midg 1.5638899E-02 3.3530068E-02 gauss-seidel spectral radius is 0.9988706 estimated iterations to convergence 235 setup time was (sec) 0.8000000 now iterating at: 06:33:35 rms-change max change #iterations 4.760256 202.8674 at 10iterations 2.386644 72.54475 at 20iterations 1.203857 37.49556 at 30iterations 0.6065836 17.82702 at 40iterations 0.3041293 9.026695 at 50iterations 0.1531820 4.306122 at 60iterations 7.6711111E-02 2.311901 at 70iterations 3.8638964E-02 1.117798 at 80iterations 1.9504735E-02 0.5580368 at 90iterations 9.9193742E-03 0.2917175 at 100iterations 5.0300010E-03 0.1398964 at 110iterations 2.5939504E-03 7.1067810E-02 at 120iterations finished qdiffx linear iterations at : 06:33:41 total time elapsed so far: 6.660000 # loops : 120 mean,max change (kT/e) : 2.5939504E-03 7.1067810E-02 energy calculations done at 6.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.830000 DelPhi exited at 06:33:42 6.829u 0.176s 0:07.50 93.2% 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 Tue Oct 11 2011 at 06:33:42 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.250680 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): -40.77900 -1.429000 ymin,ymax (A): -27.10500 17.66700 zmin,zma (A): -14.90600 34.37600 x,y,z range (A): 39.35000 44.77200 49.28200 scale (grids/A): 3.250680 object centre (A): -21.10400 -4.719000 9.735000 number of atom coordinates read : 2089 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 96.52216 90.84901 85.36719 assigned negative charge : -311.0742 centred at (gu) : 96.70239 91.44363 85.03669 start vw surface at 0.1500000 fill in re-entrant regions at 0.8100000 boundary points on vw surface= 179982 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17094 grid for indexing accessible points = 1.400000 m= 98582 mr = 134289 m= 41278 mr = 82515 m= 12448 mr = 34185 m= 2655 mr = 9738 m= 361 mr = 1996 m= 15 mr = 250 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.810000 number of dielectric boundary points 72348 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 15684 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) : 2.167120 object centre at (A) : -21.10400 -4.719000 9.735000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3324295 0.1893412 midg,1,midg; midg,igrid,midg 0.3521246 1.2901655E-02 1,midg,midg; igrid,midg,midg 0.1058494 0.3275112 gauss-seidel spectral radius is 0.9993054 estimated iterations to convergence 299 setup time was (sec) 2.090000 now iterating at: 06:33:44 rms-change max change #iterations 10.52986 328.2508 at 10iterations 6.249001 131.5561 at 20iterations 3.697352 80.08955 at 30iterations 2.186257 45.33725 at 40iterations 1.289369 24.88245 at 50iterations 0.7596177 14.46979 at 60iterations 0.4466724 7.207650 at 70iterations 0.2624303 5.426934 at 80iterations 0.1544294 3.139444 at 90iterations 9.1034517E-02 1.574906 at 100iterations 5.3612746E-02 0.9732847 at 110iterations 3.1722218E-02 0.5310917 at 120iterations 1.8874606E-02 0.3259716 at 130iterations 1.1421124E-02 0.1934004 at 140iterations 7.0628049E-03 0.1345749 at 150iterations 4.5436989E-03 8.6456299E-02 at 160iterations 3.0787741E-03 5.7884216E-02 at 170iterations 2.2131482E-03 3.9848328E-02 at 180iterations finished qdiffx linear iterations at : 06:33:53 total time elapsed so far: 11.43000 # loops : 180 mean,max change (kT/e) : 2.2131482E-03 3.9848328E-02 energy calculations done at 11.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.60000 DelPhi exited at 06:33:54 11.606u 0.168s 0:12.39 94.9% 0+0k 0+0io 0pf+0w