Sun Oct 9 14:14:51 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 Sun Oct 9 2011 at 14:14:51 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2698 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: SEP 329 has a net charge of -0.4750 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: 0.5705311 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): -7.7000022E-02 52.20500 ymin,ymax (A): -8.323000 39.83600 zmin,zma (A): -15.53300 46.86500 x,y,z range (A): 52.28200 48.15900 62.39800 scale (grids/A): 0.5705311 object centre (A): 26.06400 15.75650 15.66600 number of atom coordinates read : 2698 total number of charged atoms : 2556 net assigned charge : 6.539022 assigned positive charge : 411.2985 centred at (gu) : 89.68473 90.09482 88.47350 assigned negative charge : -404.7605 centred at (gu) : 89.64067 89.98923 88.51459 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5753 nv = 96 ne = 84 npr = 53248 no. pairs analyzed = 53248 no. exposed pairs = 3522 no. arc points = 25164 no. surface atoms = 1180 nbur = 1518 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 = 1.512000 m= 228 mr = 2849 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3125 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2553 ## 310 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7368 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3046789E-09 2.9773309E-10 midg,1,midg; midg,igrid,midg -5.2993387E-10 2.5844431E-09 1,midg,midg; igrid,midg,midg 3.9248135E-10 1.5311562E-09 gauss-seidel spectral radius is 0.9841280 estimated iterations to convergence 65 setup time was (sec) 0.5400000 now iterating at: 14:14:52 rms-change max change #iterations 8.9492075E-02 15.15466 at 10iterations 6.5298537E-03 1.204445 at 20iterations 4.8829435E-04 8.5735321E-02 at 30iterations 3.7996804E-05 5.9337616E-03 at 40iterations 3.8963303E-06 7.0667267E-04 at 50iterations finished qdiffx linear iterations at : 14:14:54 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 3.8963303E-06 7.0667267E-04 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 14:14:55 3.351u 0.153s 0:03.82 91.6% 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 Sun Oct 9 2011 at 14:14:55 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2698 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: SEP 329 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.711593 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): -7.7000022E-02 52.20500 ymin,ymax (A): -8.323000 39.83600 zmin,zma (A): -15.53300 46.86500 x,y,z range (A): 52.28200 48.15900 62.39800 scale (grids/A): 1.711593 object centre (A): 26.06400 15.75650 15.66600 number of atom coordinates read : 2698 total number of charged atoms : 2556 net assigned charge : 6.539022 assigned positive charge : 411.2985 centred at (gu) : 89.05337 90.28393 85.41972 assigned negative charge : -404.7605 centred at (gu) : 88.92171 89.96756 85.54336 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 62977 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25164 grid for indexing accessible points = 1.400000 m= 19992 mr = 41618 m= 2299 mr = 13522 m= 73 mr = 1114 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 29081 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 290 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 19758 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) : 0.5705311 object centre at (A) : 26.06400 15.75650 15.66600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.2005570E-02 1.1842748E-02 midg,1,midg; midg,igrid,midg -3.0656753E-03 4.0021692E-03 1,midg,midg; igrid,midg,midg -1.1309879E-02 -1.8320282E-03 gauss-seidel spectral radius is 0.9983338 estimated iterations to convergence 194 setup time was (sec) 0.7700000 now iterating at: 14:14:56 rms-change max change #iterations 3.504018 179.3616 at 10iterations 1.507201 60.98816 at 20iterations 0.6541301 22.55931 at 30iterations 0.2831937 11.76640 at 40iterations 0.1220255 4.677085 at 50iterations 5.2692506E-02 1.954139 at 60iterations 2.2692984E-02 0.8172913 at 70iterations 9.8483097E-03 0.3747625 at 80iterations 4.2479313E-03 0.1472702 at 90iterations 1.8440700E-03 6.3934326E-02 at 100iterations 7.9845620E-04 2.8895855E-02 at 110iterations 3.4629647E-04 1.2326241E-02 at 120iterations finished qdiffx linear iterations at : 14:15:02 total time elapsed so far: 7.260000 # loops : 120 mean,max change (kT/e) : 3.4629647E-04 1.2326241E-02 energy calculations done at 7.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 14:15:03 7.460u 0.167s 0:07.96 95.7% 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 Sun Oct 9 2011 at 14:15:03 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2698 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: SEP 329 has a net charge of -0.4750 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: 2.567390 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): -7.7000022E-02 52.20500 ymin,ymax (A): -8.323000 39.83600 zmin,zma (A): -15.53300 46.86500 x,y,z range (A): 52.28200 48.15900 62.39800 scale (grids/A): 2.567390 object centre (A): 26.06400 15.75650 15.66600 number of atom coordinates read : 2698 total number of charged atoms : 2556 net assigned charge : 6.539022 assigned positive charge : 411.2985 centred at (gu) : 88.57986 90.42566 83.12945 assigned negative charge : -404.7605 centred at (gu) : 88.38260 89.95126 83.31496 start vw surface at 0.1600000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 145877 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25164 grid for indexing accessible points = 1.400000 m= 67880 mr = 101974 m= 20398 mr = 52892 m= 3528 mr = 15206 m= 345 mr = 2224 m= 5 mr = 164 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.150000 number of dielectric boundary points 65573 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 20432 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) : 1.711593 object centre at (A) : 26.06400 15.75650 15.66600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.167485 0.1761603 midg,1,midg; midg,igrid,midg -6.3770048E-02 1.0480089E-02 1,midg,midg; igrid,midg,midg -0.1190976 -5.2492373E-02 gauss-seidel spectral radius is 0.9991812 estimated iterations to convergence 276 setup time was (sec) 1.450000 now iterating at: 14:15:05 rms-change max change #iterations 8.910452 280.9317 at 10iterations 5.137055 152.2750 at 20iterations 2.946107 78.24701 at 30iterations 1.672024 46.31645 at 40iterations 0.9474003 22.10949 at 50iterations 0.5347297 11.66908 at 60iterations 0.3011865 6.529264 at 70iterations 0.1691850 3.826070 at 80iterations 9.4853431E-02 2.007168 at 90iterations 5.3157993E-02 1.090014 at 100iterations 2.9772095E-02 0.6363735 at 110iterations 1.6677449E-02 0.3747597 at 120iterations 9.3387906E-03 0.2043915 at 130iterations 5.2136783E-03 0.1278467 at 140iterations 2.9072228E-03 5.7260513E-02 at 150iterations 1.6285992E-03 4.2534232E-02 at 160iterations 9.0953248E-04 1.8397570E-02 at 170iterations 5.0912588E-04 1.1790514E-02 at 180iterations finished qdiffx linear iterations at : 14:15:15 total time elapsed so far: 11.68000 # loops : 180 mean,max change (kT/e) : 5.0912588E-04 1.1790514E-02 energy calculations done at 11.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.88000 DelPhi exited at 14:15:15 11.880u 0.173s 0:12.42 97.0% 0+0k 0+0io 0pf+0w