Tue Oct 11 07:14:00 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 07:14:00 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2551 !!! WARNING: GLM 165 has a net charge of -0.0940 !!! WARNING: HIR 207 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6640181 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): -54.67200 -1.059000 ymin,ymax (A): -28.27100 24.06300 zmin,zma (A): -2.517000 43.89400 x,y,z range (A): 53.61300 52.33400 46.41100 scale (grids/A): 0.6640181 object centre (A): -27.86550 -2.104000 20.68850 number of atom coordinates read : 2551 total number of charged atoms : 2408 net assigned charge : -2.579994 assigned positive charge : 379.6291 centred at (gu) : 90.07341 90.88029 88.86621 assigned negative charge : -382.2095 centred at (gu) : 89.99677 90.81277 88.71689 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7683 nv = 96 ne = 84 npr = 51952 no. pairs analyzed = 51952 no. exposed pairs = 3196 no. arc points = 22091 no. surface atoms = 1096 nbur = 1455 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 506 mr = 4371 m= 4 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.2000000 number of dielectric boundary points 3741 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2034 ## 180 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8891 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.0393030E-08 1.9368262E-08 midg,1,midg; midg,igrid,midg -1.8057349E-08 9.0587209E-09 1,midg,midg; igrid,midg,midg -2.3287797E-08 9.5252695E-09 gauss-seidel spectral radius is 0.9882439 estimated iterations to convergence 75 setup time was (sec) 0.3900000 now iterating at: 07:14:01 rms-change max change #iterations 0.1718050 21.78546 at 10iterations 1.8584173E-02 2.770211 at 20iterations 2.0412349E-03 0.2572708 at 30iterations 2.5577893E-04 4.3300629E-02 at 40iterations 4.1711264E-05 7.6637268E-03 at 50iterations finished qdiffx linear iterations at : 07:14:04 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 4.1711264E-05 7.6637268E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 07:14:04 3.428u 0.187s 0:03.91 92.0% 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 Tue Oct 11 2011 at 07:14:04 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2551 !!! WARNING: GLM 165 has a net charge of -0.0940 !!! WARNING: HIR 207 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.992054 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): -54.67200 -1.059000 ymin,ymax (A): -28.27100 24.06300 zmin,zma (A): -2.517000 43.89400 x,y,z range (A): 53.61300 52.33400 46.41100 scale (grids/A): 1.992054 object centre (A): -27.86550 -2.104000 20.68850 number of atom coordinates read : 2551 total number of charged atoms : 2408 net assigned charge : -2.579994 assigned positive charge : 379.6291 centred at (gu) : 90.21980 92.64065 86.59800 assigned negative charge : -382.2095 centred at (gu) : 89.99021 92.43845 86.15034 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 82292 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22091 grid for indexing accessible points = 1.400000 m= 32003 mr = 57476 m= 5830 mr = 24571 m= 432 mr = 4031 m= 7 mr = 211 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 657 time to turn everything in is 0.4000000 number of dielectric boundary points 34275 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 110 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 19035 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) : 0.6640181 object centre at (A) : -27.86550 -2.104000 20.68850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6469812E-02 2.2380231E-02 midg,1,midg; midg,igrid,midg -3.4584325E-02 -3.7566163E-02 1,midg,midg; igrid,midg,midg -2.5174713E-02 -4.2770445E-02 gauss-seidel spectral radius is 0.9987463 estimated iterations to convergence 224 setup time was (sec) 0.6300000 now iterating at: 07:14:05 rms-change max change #iterations 4.601400 183.3700 at 10iterations 2.223618 81.51256 at 20iterations 1.073229 33.78759 at 30iterations 0.5179960 16.80272 at 40iterations 0.2509915 8.484221 at 50iterations 0.1215324 3.723198 at 60iterations 5.8766067E-02 1.776751 at 70iterations 2.8399853E-02 0.8615177 at 80iterations 1.3758305E-02 0.4611397 at 90iterations 6.6594593E-03 0.1866455 at 100iterations 3.2254572E-03 9.5666885E-02 at 110iterations 1.5636942E-03 4.4053078E-02 at 120iterations finished qdiffx linear iterations at : 07:14:12 total time elapsed so far: 7.860000 # loops : 120 mean,max change (kT/e) : 1.5636942E-03 4.4053078E-02 energy calculations done at 7.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.990000 DelPhi exited at 07:14:13 7.989u 0.223s 0:08.49 96.5% 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 07:14:13 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2551 !!! WARNING: GLM 165 has a net charge of -0.0940 !!! WARNING: HIR 207 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.988081 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): -54.67200 -1.059000 ymin,ymax (A): -28.27100 24.06300 zmin,zma (A): -2.517000 43.89400 x,y,z range (A): 53.61300 52.33400 46.41100 scale (grids/A): 2.988081 object centre (A): -27.86550 -2.104000 20.68850 number of atom coordinates read : 2551 total number of charged atoms : 2408 net assigned charge : -2.579994 assigned positive charge : 379.6291 centred at (gu) : 90.32959 93.96088 84.89685 assigned negative charge : -382.2095 centred at (gu) : 89.98523 93.65757 84.22545 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 189843 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22091 grid for indexing accessible points = 1.400000 m= 100754 mr = 138741 m= 40061 mr = 84111 m= 11085 mr = 33277 m= 1980 mr = 8843 m= 144 mr = 1474 m= 3 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.6299999 no. cavity mid-points inaccessible to solvent = 2455 time to turn everything in is 1.090000 number of dielectric boundary points 77348 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 19264 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) : 1.992054 object centre at (A) : -27.86550 -2.104000 20.68850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4002385 0.1583747 midg,1,midg; midg,igrid,midg -0.4437203 -0.5525318 1,midg,midg; igrid,midg,midg -0.1044782 -0.5475038 gauss-seidel spectral radius is 0.9992882 estimated iterations to convergence 296 setup time was (sec) 1.330000 now iterating at: 07:14:14 rms-change max change #iterations 10.50411 349.0576 at 10iterations 6.161798 138.9256 at 20iterations 3.597890 62.11064 at 30iterations 2.096848 40.02727 at 40iterations 1.221617 22.48722 at 50iterations 0.7101943 12.64564 at 60iterations 0.4133013 7.141522 at 70iterations 0.2399727 4.154878 at 80iterations 0.1392564 2.464290 at 90iterations 8.0822796E-02 1.589668 at 100iterations 4.6968251E-02 0.7790604 at 110iterations 2.7239077E-02 0.4936991 at 120iterations 1.5848514E-02 0.2978945 at 130iterations 9.1929073E-03 0.1494789 at 140iterations 5.3463266E-03 9.6153259E-02 at 150iterations 3.1080486E-03 5.0856113E-02 at 160iterations 1.8126611E-03 3.1851768E-02 at 170iterations 1.0577798E-03 1.6975403E-02 at 180iterations finished qdiffx linear iterations at : 07:14:26 total time elapsed so far: 12.99000 # loops : 180 mean,max change (kT/e) : 1.0577798E-03 1.6975403E-02 energy calculations done at 12.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.13000 DelPhi exited at 07:14:27 13.128u 0.228s 0:13.80 96.6% 0+0k 0+0io 0pf+0w