Mon Oct 10 13:59:09 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 Mon Oct 10 2011 at 13:59:09 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4436 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: 0.5064372 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): -2.887000 67.40800 ymin,ymax (A): -11.87200 39.48400 zmin,zma (A): -19.36000 46.52700 x,y,z range (A): 70.29500 51.35600 65.88699 scale (grids/A): 0.5064372 object centre (A): 32.26050 13.80600 13.58350 number of atom coordinates read : 4436 total number of charged atoms : 4281 net assigned charge : -6.499956 assigned positive charge : 669.2797 centred at (gu) : 88.19324 89.79984 90.55996 assigned negative charge : -675.7822 centred at (gu) : 88.25597 89.90648 90.59949 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7083 nv = 96 ne = 84 npr = 93204 no. pairs analyzed = 93204 no. exposed pairs = 5038 no. arc points = 33774 no. surface atoms = 1713 nbur = 2723 mkacc time = 0.1500000 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 = 1.680000 m= 236 mr = 3976 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.2900000 number of dielectric boundary points 3338 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3400 ## 540 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 9568 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0810586E-12 -1.8535205E-10 midg,1,midg; midg,igrid,midg 1.4396420E-10 -2.8410810E-10 1,midg,midg; igrid,midg,midg 8.2024186E-11 -1.2934247E-10 gauss-seidel spectral radius is 0.9800250 estimated iterations to convergence 59 setup time was (sec) 0.4900000 now iterating at: 13:59:10 rms-change max change #iterations 6.1680552E-02 9.549490 at 10iterations 3.7506702E-03 0.5792084 at 20iterations 4.7947140E-04 6.5988779E-02 at 30iterations 1.2224342E-04 1.7233610E-02 at 40iterations 3.4414374E-05 4.8999786E-03 at 50iterations finished qdiffx linear iterations at : 13:59:12 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 3.4414374E-05 4.8999786E-03 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 13:59:13 3.492u 0.175s 0:04.44 82.4% 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 Mon Oct 10 2011 at 13:59:13 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 = 4436 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: 1.519312 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): -2.887000 67.40800 ymin,ymax (A): -11.87200 39.48400 zmin,zma (A): -19.36000 46.52700 x,y,z range (A): 70.29500 51.35600 65.88699 scale (grids/A): 1.519312 object centre (A): 32.26050 13.80600 13.58350 number of atom coordinates read : 4436 total number of charged atoms : 4281 net assigned charge : -6.499956 assigned positive charge : 669.2797 centred at (gu) : 84.57880 89.39838 91.67855 assigned negative charge : -675.7822 centred at (gu) : 84.76744 89.71890 91.79787 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 81008 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33774 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 23753 mr = 58431 m= 1959 mr = 16533 m= 38 mr = 804 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1552 time to turn everything in is 0.4000000 number of dielectric boundary points 30991 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 474 ## 12 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 32109 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) : 0.5064372 object centre at (A) : 32.26050 13.80600 13.58350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.3040764E-03 -1.8719586E-02 midg,1,midg; midg,igrid,midg 2.1070389E-03 -1.0114264E-02 1,midg,midg; igrid,midg,midg 1.1330895E-02 -5.6613488E-03 gauss-seidel spectral radius is 0.9980194 estimated iterations to convergence 179 setup time was (sec) 0.6500000 now iterating at: 13:59:14 rms-change max change #iterations 3.569170 172.5982 at 10iterations 1.423248 49.68819 at 20iterations 0.5725517 19.99703 at 30iterations 0.2304426 8.725464 at 40iterations 9.2660196E-02 3.116594 at 50iterations 3.7367254E-02 1.201339 at 60iterations 1.5104751E-02 0.4986668 at 70iterations 6.1234874E-03 0.2067413 at 80iterations 2.5193589E-03 8.3059311E-02 at 90iterations 1.0683173E-03 3.5255432E-02 at 100iterations 4.7682985E-04 1.5823364E-02 at 110iterations 2.3294057E-04 7.5664520E-03 at 120iterations finished qdiffx linear iterations at : 13:59:22 total time elapsed so far: 7.880000 # loops : 120 mean,max change (kT/e) : 2.3294057E-04 7.5664520E-03 energy calculations done at 7.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.020000 DelPhi exited at 13:59:23 8.025u 0.287s 0:09.55 86.9% 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 Mon Oct 10 2011 at 13:59:23 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4436 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: 2.278967 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): -2.887000 67.40800 ymin,ymax (A): -11.87200 39.48400 zmin,zma (A): -19.36000 46.52700 x,y,z range (A): 70.29500 51.35600 65.88699 scale (grids/A): 2.278967 object centre (A): 32.26050 13.80600 13.58350 number of atom coordinates read : 4436 total number of charged atoms : 4281 net assigned charge : -6.499956 assigned positive charge : 669.2797 centred at (gu) : 81.86813 89.09721 92.51743 assigned negative charge : -675.7822 centred at (gu) : 82.15107 89.57829 92.69672 start vw surface at 0.1300000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 189435 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33774 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 86090 mr = 143153 m= 21397 mr = 69042 m= 2891 mr = 15905 m= 105 mr = 1733 m= 0 mr = 17 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 5273 time to turn everything in is 0.9600000 number of dielectric boundary points 70068 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 59 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 34141 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) : 1.519312 object centre at (A) : 32.26050 13.80600 13.58350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2589965 -0.3962985 midg,1,midg; midg,igrid,midg 2.4689697E-02 -0.1684509 1,midg,midg; igrid,midg,midg 0.2941103 -0.5063501 gauss-seidel spectral radius is 0.9991114 estimated iterations to convergence 265 setup time was (sec) 1.210000 now iterating at: 13:59:24 rms-change max change #iterations 9.583494 332.2266 at 10iterations 5.349985 131.7378 at 20iterations 2.971946 71.95641 at 30iterations 1.648096 34.51237 at 40iterations 0.9039937 19.52314 at 50iterations 0.4972398 9.689365 at 60iterations 0.2728274 5.498627 at 70iterations 0.1494933 2.870033 at 80iterations 8.1862666E-02 1.546537 at 90iterations 4.4733267E-02 0.8329458 at 100iterations 2.4482431E-02 0.5059948 at 110iterations 1.3388688E-02 0.2707443 at 120iterations 7.3151058E-03 0.1372070 at 130iterations 4.0112389E-03 8.1849098E-02 at 140iterations 2.2075656E-03 4.1252136E-02 at 150iterations 1.2259132E-03 2.5151253E-02 at 160iterations 6.8935455E-04 1.3053894E-02 at 170iterations 3.9618515E-04 8.0471039E-03 at 180iterations finished qdiffx linear iterations at : 13:59:36 total time elapsed so far: 12.94000 # loops : 180 mean,max change (kT/e) : 3.9618515E-04 8.0471039E-03 energy calculations done at 12.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.08000 DelPhi exited at 13:59:37 13.083u 0.219s 0:13.73 96.7% 0+0k 0+0io 0pf+0w