Mon Oct 10 19:38:24 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 Mon Oct 10 2011 at 19:38:24 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2875 !!! WARNING: SEP 69 has a net charge of -0.4750 !!! WARNING: HIR 103 has a net charge of 0.5140 !!! WARNING: HIR 229 has a net charge of 0.5140 !!! WARNING: CME 1 has a net charge of -0.0350 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: 0.6264628 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): -42.94100 10.51400 ymin,ymax (A): -15.99100 40.43300 zmin,zma (A): -46.05800 10.76900 x,y,z range (A): 53.45500 56.42400 56.82700 scale (grids/A): 0.6264628 object centre (A): -16.21350 12.22100 -17.64450 number of atom coordinates read : 2875 total number of charged atoms : 2729 net assigned charge : -3.481992 assigned positive charge : 435.1743 centred at (gu) : 91.09561 89.42952 89.60115 assigned negative charge : -438.6576 centred at (gu) : 91.11852 89.45702 89.61164 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7605 nv = 96 ne = 84 npr = 57670 no. pairs analyzed = 57670 no. exposed pairs = 3989 no. arc points = 28419 no. surface atoms = 1310 nbur = 1565 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 399 mr = 3795 m= 3 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 4178 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2746 ## 236 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9159 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6627207E-09 -3.9937071E-09 midg,1,midg; midg,igrid,midg -1.0214053E-09 -5.2105893E-09 1,midg,midg; igrid,midg,midg -1.0815825E-09 -6.9400463E-09 gauss-seidel spectral radius is 0.9868401 estimated iterations to convergence 71 setup time was (sec) 0.6100000 now iterating at: 19:38:25 rms-change max change #iterations 0.1390816 22.10472 at 10iterations 1.3017743E-02 1.759804 at 20iterations 1.2400950E-03 0.1552315 at 30iterations 1.1858347E-04 1.6485214E-02 at 40iterations 1.2261420E-05 1.8806458E-03 at 50iterations finished qdiffx linear iterations at : 19:38:28 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.2261420E-05 1.8806458E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 19:38:28 3.487u 0.177s 0:04.24 86.0% 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 19:38:29 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2875 !!! WARNING: SEP 69 has a net charge of -0.4750 !!! WARNING: HIR 103 has a net charge of 0.5140 !!! WARNING: HIR 229 has a net charge of 0.5140 !!! WARNING: CME 1 has a net charge of -0.0350 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.879388 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): -42.94100 10.51400 ymin,ymax (A): -15.99100 40.43300 zmin,zma (A): -46.05800 10.76900 x,y,z range (A): 53.45500 56.42400 56.82700 scale (grids/A): 1.879388 object centre (A): -16.21350 12.22100 -17.64450 number of atom coordinates read : 2875 total number of charged atoms : 2729 net assigned charge : -3.481992 assigned positive charge : 435.1743 centred at (gu) : 93.28604 88.28775 88.80270 assigned negative charge : -438.6576 centred at (gu) : 93.35526 88.37076 88.83471 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 82290 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28419 grid for indexing accessible points = 1.400000 m= 27536 mr = 54037 m= 4100 mr = 18967 m= 188 mr = 2208 m= 3 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 38864 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 168 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 21437 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) : 0.6264628 object centre at (A) : -16.21350 12.22100 -17.64450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8503388E-02 -8.8275801E-03 midg,1,midg; midg,igrid,midg -3.0687952E-03 -3.2674260E-03 1,midg,midg; igrid,midg,midg -3.8002960E-03 6.3377325E-03 gauss-seidel spectral radius is 0.9986466 estimated iterations to convergence 215 setup time was (sec) 0.9400000 now iterating at: 19:38:30 rms-change max change #iterations 4.478574 220.9669 at 10iterations 2.092535 72.87197 at 20iterations 0.9764490 30.58990 at 30iterations 0.4584374 13.92555 at 40iterations 0.2152622 7.259634 at 50iterations 0.1008230 3.094577 at 60iterations 4.7350742E-02 1.504711 at 70iterations 2.2197144E-02 0.7669735 at 80iterations 1.0372832E-02 0.3251839 at 90iterations 4.8869601E-03 0.1447325 at 100iterations 2.2936030E-03 7.2322369E-02 at 110iterations 1.0797523E-03 3.4160614E-02 at 120iterations finished qdiffx linear iterations at : 19:38:37 total time elapsed so far: 7.970000 # loops : 120 mean,max change (kT/e) : 1.0797523E-03 3.4160614E-02 energy calculations done at 7.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.160000 DelPhi exited at 19:38:37 8.163u 0.235s 0:08.74 95.9% 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 19:38:37 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2875 !!! WARNING: SEP 69 has a net charge of -0.4750 !!! WARNING: HIR 103 has a net charge of 0.5140 !!! WARNING: HIR 229 has a net charge of 0.5140 !!! WARNING: CME 1 has a net charge of -0.0350 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.819082 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): -42.94100 10.51400 ymin,ymax (A): -15.99100 40.43300 zmin,zma (A): -46.05800 10.76900 x,y,z range (A): 53.45500 56.42400 56.82700 scale (grids/A): 2.819082 object centre (A): -16.21350 12.22100 -17.64450 number of atom coordinates read : 2875 total number of charged atoms : 2729 net assigned charge : -3.481992 assigned positive charge : 435.1743 centred at (gu) : 94.92878 87.43157 88.20396 assigned negative charge : -438.6576 centred at (gu) : 95.03293 87.55621 88.25213 start vw surface at 0.2000000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 190494 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28419 grid for indexing accessible points = 1.400000 m= 89557 mr = 132260 m= 31082 mr = 70301 m= 6964 mr = 23563 m= 818 mr = 4751 m= 31 mr = 466 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.620000 number of dielectric boundary points 87602 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 21829 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) : 1.879388 object centre at (A) : -16.21350 12.22100 -17.64450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3763171 -7.3872432E-02 midg,1,midg; midg,igrid,midg -3.2583398E-03 2.0016305E-02 1,midg,midg; igrid,midg,midg -6.0970176E-02 0.2183740 gauss-seidel spectral radius is 0.9992814 estimated iterations to convergence 294 setup time was (sec) 1.950000 now iterating at: 19:38:39 rms-change max change #iterations 10.67475 335.1160 at 10iterations 6.345786 143.3708 at 20iterations 3.748347 81.05024 at 30iterations 2.198936 42.86351 at 40iterations 1.288393 27.15025 at 50iterations 0.7521775 12.86893 at 60iterations 0.4387650 9.034214 at 70iterations 0.2551493 4.930886 at 80iterations 0.1481214 2.792896 at 90iterations 8.6064629E-02 1.532051 at 100iterations 4.9947891E-02 0.8955064 at 110iterations 2.9001351E-02 0.5238997 at 120iterations 1.6813289E-02 0.3064079 at 130iterations 9.7417692E-03 0.1668148 at 140iterations 5.6468807E-03 9.8426819E-02 at 150iterations 3.2717651E-03 5.8289528E-02 at 160iterations 1.9010386E-03 3.2302856E-02 at 170iterations 1.1026323E-03 1.9467354E-02 at 180iterations finished qdiffx linear iterations at : 19:38:51 total time elapsed so far: 13.36000 # loops : 180 mean,max change (kT/e) : 1.1026323E-03 1.9467354E-02 energy calculations done at 13.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.55000 DelPhi exited at 19:38:52 13.551u 0.235s 0:14.27 96.5% 0+0k 0+0io 0pf+0w