Mon Oct 10 14:07:13 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 14:07:13 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3867 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: 0.5423853 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): -4.807000 55.89800 ymin,ymax (A): -27.11400 38.52200 zmin,zma (A): -10.66500 41.99200 x,y,z range (A): 60.70500 65.63600 52.65700 scale (grids/A): 0.5423853 object centre (A): 25.54550 5.704001 15.66350 number of atom coordinates read : 3867 total number of charged atoms : 3723 net assigned charge : -3.499993 assigned positive charge : 598.7670 centred at (gu) : 91.26637 91.03024 91.08694 assigned negative charge : -602.2698 centred at (gu) : 91.22853 91.11707 90.97311 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7380 nv = 96 ne = 84 npr = 77514 no. pairs analyzed = 77514 no. exposed pairs = 4954 no. arc points = 33980 no. surface atoms = 1670 nbur = 2197 mkacc time = 0.1300000 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= 301 mr = 3834 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.2700000 number of dielectric boundary points 3826 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3426 ## 426 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 9715 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.3778334E-10 9.0542407E-10 midg,1,midg; midg,igrid,midg 3.6692729E-10 -1.1443705E-09 1,midg,midg; igrid,midg,midg -3.6020742E-10 1.4227791E-10 gauss-seidel spectral radius is 0.9825453 estimated iterations to convergence 62 setup time was (sec) 0.4600000 now iterating at: 14:07:14 rms-change max change #iterations 8.3382756E-02 12.75185 at 10iterations 5.9423721E-03 0.8709068 at 20iterations 7.7179912E-04 0.1401501 at 30iterations 1.8765651E-04 3.6724091E-02 at 40iterations 5.2617175E-05 1.0055542E-02 at 50iterations finished qdiffx linear iterations at : 14:07:17 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 5.2617175E-05 1.0055542E-02 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 14:07:18 3.456u 0.208s 0:04.27 85.4% 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 14:07:18 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3867 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: 1.627156 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): -4.807000 55.89800 ymin,ymax (A): -27.11400 38.52200 zmin,zma (A): -10.66500 41.99200 x,y,z range (A): 60.70500 65.63600 52.65700 scale (grids/A): 1.627156 object centre (A): 25.54550 5.704001 15.66350 number of atom coordinates read : 3867 total number of charged atoms : 3723 net assigned charge : -3.499993 assigned positive charge : 598.7670 centred at (gu) : 93.79816 93.08955 93.25926 assigned negative charge : -602.2698 centred at (gu) : 93.68544 93.35107 92.91926 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 82473 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33980 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 25313 mr = 56671 m= 2752 mr = 16975 m= 80 mr = 1295 m= 0 mr = 12 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 821 time to turn everything in is 0.4000000 number of dielectric boundary points 35665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 343 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 28506 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) : 0.5423853 object centre at (A) : 25.54550 5.704001 15.66350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5650375E-02 -4.7366158E-03 midg,1,midg; midg,igrid,midg 2.3173058E-02 -9.8651871E-03 1,midg,midg; igrid,midg,midg 3.8334972E-03 -8.0860304E-03 gauss-seidel spectral radius is 0.9982683 estimated iterations to convergence 191 setup time was (sec) 0.6100000 now iterating at: 14:07:19 rms-change max change #iterations 3.917640 153.9827 at 10iterations 1.658887 54.66703 at 20iterations 0.7091353 24.11615 at 30iterations 0.3023324 9.496901 at 40iterations 0.1285763 4.161476 at 50iterations 5.4776058E-02 1.941710 at 60iterations 2.3378124E-02 0.7247943 at 70iterations 1.0016072E-02 0.3459682 at 80iterations 4.3125604E-03 0.1364594 at 90iterations 1.8790526E-03 6.0564041E-02 at 100iterations 8.3936140E-04 3.0756474E-02 at 110iterations 3.9379986E-04 1.3767242E-02 at 120iterations finished qdiffx linear iterations at : 14:07:26 total time elapsed so far: 8.380000 # loops : 120 mean,max change (kT/e) : 3.9379986E-04 1.3767242E-02 energy calculations done at 8.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.520000 DelPhi exited at 14:07:27 8.521u 0.388s 0:09.55 93.1% 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 14:07:27 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3867 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: 2.440734 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): -4.807000 55.89800 ymin,ymax (A): -27.11400 38.52200 zmin,zma (A): -10.66500 41.99200 x,y,z range (A): 60.70500 65.63600 52.65700 scale (grids/A): 2.440734 object centre (A): 25.54550 5.704001 15.66350 number of atom coordinates read : 3867 total number of charged atoms : 3723 net assigned charge : -3.499993 assigned positive charge : 598.7670 centred at (gu) : 95.69688 94.63403 94.88846 assigned negative charge : -602.2698 centred at (gu) : 95.52801 95.02629 94.37874 start vw surface at 0.1200000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 191964 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33980 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 88024 mr = 139275 m= 24854 mr = 68591 m= 4227 mr = 18187 m= 299 mr = 2717 m= 10 mr = 134 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 2678 time to turn everything in is 1.020000 number of dielectric boundary points 80474 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 29750 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) : 1.627156 object centre at (A) : 25.54550 5.704001 15.66350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2211548 -0.1189072 midg,1,midg; midg,igrid,midg 0.6404070 -0.2185237 1,midg,midg; igrid,midg,midg 0.1131490 -0.1851783 gauss-seidel spectral radius is 0.9991864 estimated iterations to convergence 277 setup time was (sec) 1.260000 now iterating at: 14:07:29 rms-change max change #iterations 10.31557 343.3188 at 10iterations 5.929622 134.2509 at 20iterations 3.401599 98.51509 at 30iterations 1.939220 45.90277 at 40iterations 1.099147 21.24409 at 50iterations 0.6234383 12.89692 at 60iterations 0.3512833 6.581353 at 70iterations 0.1983036 3.490749 at 80iterations 0.1115192 2.050152 at 90iterations 6.2726855E-02 1.219894 at 100iterations 3.5274401E-02 0.6571808 at 110iterations 1.9825164E-02 0.3566799 at 120iterations 1.1133727E-02 0.2135353 at 130iterations 6.2419227E-03 0.1192322 at 140iterations 3.5125357E-03 6.7184448E-02 at 150iterations 1.9774272E-03 3.5915375E-02 at 160iterations 1.1176398E-03 2.0102501E-02 at 170iterations 6.3605886E-04 1.2948871E-02 at 180iterations finished qdiffx linear iterations at : 14:07:42 total time elapsed so far: 12.94000 # loops : 180 mean,max change (kT/e) : 6.3605886E-04 1.2948871E-02 energy calculations done at 12.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.07000 DelPhi exited at 14:07:43 13.071u 1.351s 0:15.47 93.2% 0+0k 0+0io 0pf+0w