Tue Oct 11 03:47:59 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 Tue Oct 11 2011 at 03:48:00 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2760 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3590 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: 0.6224538 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): -46.07000 1.059000 ymin,ymax (A): -47.32800 1.670000 zmin,zma (A): -11.33200 45.86100 x,y,z range (A): 47.12900 48.99800 57.19300 scale (grids/A): 0.6224538 object centre (A): -22.50550 -22.82900 17.26450 number of atom coordinates read : 2760 total number of charged atoms : 2606 net assigned charge : 1.155017 assigned positive charge : 420.4458 centred at (gu) : 89.99500 90.38983 92.03140 assigned negative charge : -419.2912 centred at (gu) : 89.74396 90.20518 91.88531 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7143 nv = 96 ne = 84 npr = 56176 no. pairs analyzed = 56176 no. exposed pairs = 3329 no. arc points = 23113 no. surface atoms = 1124 nbur = 1636 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 388 mr = 4054 m= 2 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.3300000 number of dielectric boundary points 3431 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2416 ## 271 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8766 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.7954393E-09 1.8607766E-08 midg,1,midg; midg,igrid,midg -1.2596806E-08 1.5954226E-08 1,midg,midg; igrid,midg,midg -1.9123156E-08 1.9458680E-08 gauss-seidel spectral radius is 0.9866446 estimated iterations to convergence 71 setup time was (sec) 0.5700000 now iterating at: 03:48:00 rms-change max change #iterations 0.1339204 21.26478 at 10iterations 1.2416960E-02 1.681755 at 20iterations 1.1876876E-03 0.1868134 at 30iterations 1.2305514E-04 1.7156601E-02 at 40iterations 1.7860340E-05 2.2277832E-03 at 50iterations finished qdiffx linear iterations at : 03:48:03 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 1.7860340E-05 2.2277832E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 03:48:03 3.435u 0.175s 0:03.97 90.6% 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 Tue Oct 11 2011 at 03:48:04 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2760 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3590 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: 1.867361 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): -46.07000 1.059000 ymin,ymax (A): -47.32800 1.670000 zmin,zma (A): -11.33200 45.86100 x,y,z range (A): 47.12900 48.99800 57.19300 scale (grids/A): 1.867361 object centre (A): -22.50550 -22.82900 17.26450 number of atom coordinates read : 2760 total number of charged atoms : 2606 net assigned charge : 1.155017 assigned positive charge : 420.4458 centred at (gu) : 89.98431 91.16904 96.09345 assigned negative charge : -419.2912 centred at (gu) : 89.23151 90.61509 95.65568 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77544 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23113 grid for indexing accessible points = 1.400000 m= 28640 mr = 54837 m= 4415 mr = 21377 m= 244 mr = 2765 m= 3 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 643 time to turn everything in is 0.5700000 number of dielectric boundary points 31793 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 183 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 20459 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) : 0.6224538 object centre at (A) : -22.50550 -22.82900 17.26450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.7067124E-02 8.2949577E-03 midg,1,midg; midg,igrid,midg -1.1485162E-02 2.9893216E-02 1,midg,midg; igrid,midg,midg -1.3961381E-02 4.2464465E-02 gauss-seidel spectral radius is 0.9985968 estimated iterations to convergence 212 setup time was (sec) 0.8600000 now iterating at: 03:48:05 rms-change max change #iterations 4.278683 189.1909 at 10iterations 1.984135 71.13827 at 20iterations 0.9232922 29.99342 at 30iterations 0.4272722 14.54063 at 40iterations 0.1990945 6.528986 at 50iterations 9.2639290E-02 2.770016 at 60iterations 4.3034952E-02 1.411856 at 70iterations 1.9915884E-02 0.5849791 at 80iterations 9.2839450E-03 0.2888184 at 90iterations 4.3221144E-03 0.1469727 at 100iterations 2.0151269E-03 6.5016747E-02 at 110iterations 9.3991525E-04 2.7070999E-02 at 120iterations finished qdiffx linear iterations at : 03:48:11 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 9.3991525E-04 2.7070999E-02 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.710000 DelPhi exited at 03:48:12 7.709u 0.218s 0:08.39 94.2% 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 Tue Oct 11 2011 at 03:48:12 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2760 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3590 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: 2.801042 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): -46.07000 1.059000 ymin,ymax (A): -47.32800 1.670000 zmin,zma (A): -11.33200 45.86100 x,y,z range (A): 47.12900 48.99800 57.19300 scale (grids/A): 2.801042 object centre (A): -22.50550 -22.82900 17.26450 number of atom coordinates read : 2760 total number of charged atoms : 2606 net assigned charge : 1.155017 assigned positive charge : 420.4458 centred at (gu) : 89.97636 91.75351 99.13984 assigned negative charge : -419.2912 centred at (gu) : 88.84721 90.92262 98.48335 start vw surface at 0.1800000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 179256 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23113 grid for indexing accessible points = 1.400000 m= 93039 mr = 132550 m= 33571 mr = 77014 m= 8015 mr = 27093 m= 1091 mr = 5984 m= 59 mr = 745 m= 0 mr = 12 time to grow re-entrant surface = 0.8700001 no. cavity mid-points inaccessible to solvent = 2363 time to turn everything in is 1.490000 number of dielectric boundary points 71633 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 20848 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) : 1.867361 object centre at (A) : -22.50550 -22.82900 17.26450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.065232 0.3575104 midg,1,midg; midg,igrid,midg -0.1398404 0.3494738 1,midg,midg; igrid,midg,midg -0.1198971 0.3610983 gauss-seidel spectral radius is 0.9992474 estimated iterations to convergence 288 setup time was (sec) 1.810000 now iterating at: 03:48:14 rms-change max change #iterations 10.14169 341.7824 at 10iterations 5.920186 133.1624 at 20iterations 3.447333 85.13258 at 30iterations 1.993848 40.12466 at 40iterations 1.150586 22.54196 at 50iterations 0.6638529 12.43164 at 60iterations 0.3815212 7.307638 at 70iterations 0.2196447 3.912003 at 80iterations 0.1262274 2.278664 at 90iterations 7.2485954E-02 1.282953 at 100iterations 4.1556090E-02 0.7406396 at 110iterations 2.3834407E-02 0.4102554 at 120iterations 1.3686751E-02 0.2332461 at 130iterations 7.8401091E-03 0.1413651 at 140iterations 4.5112981E-03 8.4374428E-02 at 150iterations 2.5866856E-03 4.3903351E-02 at 160iterations 1.4934005E-03 2.7632236E-02 at 170iterations 8.6953590E-04 1.6302109E-02 at 180iterations finished qdiffx linear iterations at : 03:48:24 total time elapsed so far: 12.20000 # loops : 180 mean,max change (kT/e) : 8.6953590E-04 1.6302109E-02 energy calculations done at 12.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.41000 DelPhi exited at 03:48:25 12.408u 0.191s 0:13.00 96.8% 0+0k 0+0io 0pf+0w