Sat Oct 8 17:14:18 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 8 2011 at 17:14:18 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3483 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: 0.5537926 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): 37.40600 93.44300 ymin,ymax (A): 16.41200 80.69600 zmin,zma (A): -22.94800 24.83900 x,y,z range (A): 56.03700 64.28400 47.78700 scale (grids/A): 0.5537926 object centre (A): 65.42450 48.55400 0.9454994 number of atom coordinates read : 3483 total number of charged atoms : 3337 net assigned charge : -5.999988 assigned positive charge : 527.7452 centred at (gu) : 90.49990 89.87624 89.91455 assigned negative charge : -533.7468 centred at (gu) : 90.51134 89.85003 89.88976 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7001 nv = 96 ne = 84 npr = 70215 no. pairs analyzed = 70215 no. exposed pairs = 4356 no. arc points = 30063 no. surface atoms = 1475 nbur = 2008 mkacc time = 0.1900000 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 = 1.568000 m= 286 mr = 3747 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3522 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3067 ## 395 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9099 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.8493723E-10 -2.3626329E-10 midg,1,midg; midg,igrid,midg -8.0783269E-10 -2.1977067E-10 1,midg,midg; igrid,midg,midg -3.4043657E-10 -7.0588341E-10 gauss-seidel spectral radius is 0.9832219 estimated iterations to convergence 64 setup time was (sec) 0.6300000 now iterating at: 17:14:19 rms-change max change #iterations 8.7248102E-02 14.65974 at 10iterations 6.1021266E-03 0.8504829 at 20iterations 4.9872993E-04 8.5563660E-02 at 30iterations 7.7748569E-05 1.6702652E-02 at 40iterations 2.0260688E-05 4.7059059E-03 at 50iterations finished qdiffx linear iterations at : 17:14:23 total time elapsed so far: 4.380000 # loops : 50 mean,max change (kT/e) : 2.0260688E-05 4.7059059E-03 energy calculations done at 4.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.550000 DelPhi exited at 17:14:23 4.555u 0.406s 0:05.22 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 Sat Oct 8 2011 at 17:14:23 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3483 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: 1.661378 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): 37.40600 93.44300 ymin,ymax (A): 16.41200 80.69600 zmin,zma (A): -22.94800 24.83900 x,y,z range (A): 56.03700 64.28400 47.78700 scale (grids/A): 1.661378 object centre (A): 65.42450 48.55400 0.9454994 number of atom coordinates read : 3483 total number of charged atoms : 3337 net assigned charge : -5.999988 assigned positive charge : 527.7452 centred at (gu) : 91.49876 89.62765 89.74281 assigned negative charge : -533.7468 centred at (gu) : 91.53368 89.54978 89.66884 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77133 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30063 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 25323 mr = 53408 m= 2773 mr = 17760 m= 69 mr = 1391 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 357 time to turn everything in is 0.6300000 number of dielectric boundary points 32739 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 383 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 25656 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) : 0.5537926 object centre at (A) : 65.42450 48.55400 0.9454994 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.0401359E-03 -2.4562036E-03 midg,1,midg; midg,igrid,midg 9.2833275E-03 1.9105805E-02 1,midg,midg; igrid,midg,midg -1.6336039E-02 -8.9387819E-03 gauss-seidel spectral radius is 0.9982982 estimated iterations to convergence 192 setup time was (sec) 0.9300000 now iterating at: 17:14:25 rms-change max change #iterations 3.823887 177.5295 at 10iterations 1.635684 63.97046 at 20iterations 0.7017854 23.07208 at 30iterations 0.3007389 9.213326 at 40iterations 0.1286009 4.343917 at 50iterations 5.5208039E-02 1.798313 at 60iterations 2.3813173E-02 0.8232961 at 70iterations 1.0203240E-02 0.3367472 at 80iterations 4.4006198E-03 0.1426964 at 90iterations 1.9047391E-03 6.5528303E-02 at 100iterations 8.3342177E-04 2.9708862E-02 at 110iterations 3.7463062E-04 1.2809753E-02 at 120iterations finished qdiffx linear iterations at : 17:14:34 total time elapsed so far: 10.69000 # loops : 120 mean,max change (kT/e) : 3.7463062E-04 1.2809753E-02 energy calculations done at 10.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.87000 DelPhi exited at 17:14:35 10.873u 0.442s 0:11.61 97.4% 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 Sat Oct 8 2011 at 17:14:35 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3483 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: 2.492067 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): 37.40600 93.44300 ymin,ymax (A): 16.41200 80.69600 zmin,zma (A): -22.94800 24.83900 x,y,z range (A): 56.03700 64.28400 47.78700 scale (grids/A): 2.492067 object centre (A): 65.42450 48.55400 0.9454994 number of atom coordinates read : 3483 total number of charged atoms : 3337 net assigned charge : -5.999988 assigned positive charge : 527.7452 centred at (gu) : 92.24787 89.44089 89.61378 assigned negative charge : -533.7468 centred at (gu) : 92.30025 89.32442 89.50322 start vw surface at 0.1400000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 179103 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30063 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 86546 mr = 130386 m= 25853 mr = 69289 m= 4382 mr = 19690 m= 318 mr = 2903 m= 5 mr = 119 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 1214 time to turn everything in is 1.580000 number of dielectric boundary points 73820 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 26671 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) : 1.661378 object centre at (A) : 65.42450 48.55400 0.9454994 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.6520520E-02 -7.2428104E-03 midg,1,midg; midg,igrid,midg 0.2726986 0.5212616 1,midg,midg; igrid,midg,midg -0.2410186 -7.7228613E-02 gauss-seidel spectral radius is 0.9991831 estimated iterations to convergence 276 setup time was (sec) 1.950000 now iterating at: 17:14:37 rms-change max change #iterations 9.721328 283.8636 at 10iterations 5.511965 120.2471 at 20iterations 3.121764 67.71729 at 30iterations 1.756456 36.95540 at 40iterations 0.9919986 21.23127 at 50iterations 0.5546062 11.25689 at 60iterations 0.3107998 6.797483 at 70iterations 0.1743375 3.419698 at 80iterations 9.7456485E-02 1.707008 at 90iterations 5.4588005E-02 1.065172 at 100iterations 3.0483350E-02 0.5529137 at 110iterations 1.7024107E-02 0.3160940 at 120iterations 9.5257862E-03 0.1831970 at 130iterations 5.3268932E-03 9.7107887E-02 at 140iterations 2.9810227E-03 5.6350708E-02 at 150iterations 1.6690288E-03 3.0939102E-02 at 160iterations 9.3799230E-04 1.8575668E-02 at 170iterations 5.2988302E-04 9.8099709E-03 at 180iterations finished qdiffx linear iterations at : 17:14:53 total time elapsed so far: 17.92000 # loops : 180 mean,max change (kT/e) : 5.2988302E-04 9.8099709E-03 energy calculations done at 17.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.08000 DelPhi exited at 17:14:54 18.087u 0.482s 0:18.84 98.5% 0+0k 0+0io 0pf+0w