Tue Oct 11 04:30:21 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 04:30:21 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2744 !!! WARNING: HIR 71 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6373760 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): -11.66700 36.58200 ymin,ymax (A): -25.74800 22.54300 zmin,zma (A): -10.40100 45.45300 x,y,z range (A): 48.24900 48.29100 55.85400 scale (grids/A): 0.6373760 object centre (A): 12.45750 -1.602500 17.52600 number of atom coordinates read : 2744 total number of charged atoms : 2596 net assigned charge : 3.514013 assigned positive charge : 420.1587 centred at (gu) : 90.19525 90.34333 92.02827 assigned negative charge : -416.6452 centred at (gu) : 89.93991 90.17525 91.98482 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7262 nv = 96 ne = 84 npr = 56701 no. pairs analyzed = 56701 no. exposed pairs = 3336 no. arc points = 23168 no. surface atoms = 1120 nbur = 1624 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 377 mr = 4048 m= 0 mr = 35 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3556 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2350 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8927 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7495115E-10 1.4794486E-08 midg,1,midg; midg,igrid,midg -1.4216917E-08 2.5515906E-08 1,midg,midg; igrid,midg,midg -2.4857989E-08 3.4799811E-08 gauss-seidel spectral radius is 0.9872553 estimated iterations to convergence 72 setup time was (sec) 0.4300000 now iterating at: 04:30:22 rms-change max change #iterations 0.1517657 20.85762 at 10iterations 1.5228637E-02 2.278996 at 20iterations 1.6005824E-03 0.2464581 at 30iterations 1.7949347E-04 2.8194427E-02 at 40iterations 2.8496288E-05 4.0950775E-03 at 50iterations finished qdiffx linear iterations at : 04:30:25 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 2.8496288E-05 4.0950775E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 04:30:25 3.442u 0.159s 0:04.14 86.7% 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 Tue Oct 11 2011 at 04:30:25 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2744 !!! WARNING: HIR 71 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.912128 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): -11.66700 36.58200 ymin,ymax (A): -25.74800 22.54300 zmin,zma (A): -10.40100 45.45300 x,y,z range (A): 48.24900 48.29100 55.85400 scale (grids/A): 1.912128 object centre (A): 12.45750 -1.602500 17.52600 number of atom coordinates read : 2744 total number of charged atoms : 2596 net assigned charge : 3.514013 assigned positive charge : 420.1587 centred at (gu) : 90.58506 91.02937 96.08419 assigned negative charge : -416.6452 centred at (gu) : 89.81942 90.52532 95.95403 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79538 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23168 grid for indexing accessible points = 1.400000 m= 28442 mr = 55903 m= 4100 mr = 20956 m= 196 mr = 2532 m= 1 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1957 time to turn everything in is 0.3900000 number of dielectric boundary points 32829 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 167 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 20429 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) : 0.6373760 object centre at (A) : 12.45750 -1.602500 17.52600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8910572E-02 4.7775502E-03 midg,1,midg; midg,igrid,midg -1.2653549E-02 2.6580483E-02 1,midg,midg; igrid,midg,midg -8.1344377E-03 5.6067329E-02 gauss-seidel spectral radius is 0.9986573 estimated iterations to convergence 216 setup time was (sec) 0.6000000 now iterating at: 04:30:26 rms-change max change #iterations 4.494231 182.4503 at 10iterations 2.118965 76.33058 at 20iterations 1.002714 33.25008 at 30iterations 0.4735074 15.02827 at 40iterations 0.2229276 6.945478 at 50iterations 0.1054015 3.212114 at 60iterations 4.9671151E-02 1.424366 at 70iterations 2.3552328E-02 0.7503319 at 80iterations 1.1137918E-02 0.3591223 at 90iterations 5.2497243E-03 0.1680450 at 100iterations 2.4889617E-03 7.4321747E-02 at 110iterations 1.1791042E-03 4.0557861E-02 at 120iterations finished qdiffx linear iterations at : 04:30:33 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 1.1791042E-03 4.0557861E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 04:30:34 7.867u 0.210s 0:08.45 95.5% 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 04:30:34 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2744 !!! WARNING: HIR 71 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.868192 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): -11.66700 36.58200 ymin,ymax (A): -25.74800 22.54300 zmin,zma (A): -10.40100 45.45300 x,y,z range (A): 48.24900 48.29100 55.85400 scale (grids/A): 2.868192 object centre (A): 12.45750 -1.602500 17.52600 number of atom coordinates read : 2744 total number of charged atoms : 2596 net assigned charge : 3.514013 assigned positive charge : 420.1587 centred at (gu) : 90.87733 91.54379 99.12608 assigned negative charge : -416.6452 centred at (gu) : 89.72900 90.78811 98.93093 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 183760 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23168 grid for indexing accessible points = 1.400000 m= 92982 mr = 135021 m= 32709 mr = 76425 m= 7273 mr = 26185 m= 891 mr = 5363 m= 43 mr = 569 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 6890 time to turn everything in is 1.010000 number of dielectric boundary points 74079 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 20766 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) : 1.912128 object centre at (A) : 12.45750 -1.602500 17.52600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5547673 0.2981100 midg,1,midg; midg,igrid,midg -0.1396342 0.3003445 1,midg,midg; igrid,midg,midg -3.2552183E-02 0.4897127 gauss-seidel spectral radius is 0.9992620 estimated iterations to convergence 291 setup time was (sec) 1.240000 now iterating at: 04:30:35 rms-change max change #iterations 10.45372 377.5380 at 10iterations 6.100502 130.9981 at 20iterations 3.554647 80.59691 at 30iterations 2.065362 43.27876 at 40iterations 1.196633 21.79130 at 50iterations 0.6922062 12.34096 at 60iterations 0.3997260 7.419569 at 70iterations 0.2310056 4.068195 at 80iterations 0.1334578 2.260471 at 90iterations 7.7152133E-02 1.394522 at 100iterations 4.4458650E-02 0.8797235 at 110iterations 2.5691567E-02 0.4528799 at 120iterations 1.4803359E-02 0.2575750 at 130iterations 8.5638613E-03 0.1501756 at 140iterations 4.9751573E-03 8.9942932E-02 at 150iterations 2.8992307E-03 5.2452087E-02 at 160iterations 1.7005334E-03 3.1044006E-02 at 170iterations 1.0101373E-03 1.8539429E-02 at 180iterations finished qdiffx linear iterations at : 04:30:47 total time elapsed so far: 12.69000 # loops : 180 mean,max change (kT/e) : 1.0101373E-03 1.8539429E-02 energy calculations done at 12.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.83000 DelPhi exited at 04:30:47 12.834u 0.203s 0:13.31 97.8% 0+0k 0+0io 0pf+0w