Mon Oct 10 19:38:41 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+sph.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 = amb.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 19:38:41 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2923 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: 0.5889165 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): -4.351000 46.58900 ymin,ymax (A): -25.91800 34.53200 zmin,zma (A): -14.69100 37.85100 x,y,z range (A): 50.94000 60.45000 52.54200 scale (grids/A): 0.5889165 object centre (A): 21.11900 4.306999 11.58000 number of atom coordinates read : 2923 total number of charged atoms : 2782 net assigned charge : 2.000025 assigned positive charge : 434.0884 centred at (gu) : 90.03698 90.36149 89.76837 assigned negative charge : -432.0894 centred at (gu) : 90.08121 90.52959 89.90651 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6739 nv = 96 ne = 84 npr = 58736 no. pairs analyzed = 58736 no. exposed pairs = 3653 no. arc points = 25958 no. surface atoms = 1234 nbur = 1689 mkacc time = 9.9999994E-02 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 = 1.456000 m= 300 mr = 3574 m= 3 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.2100000 number of dielectric boundary points 3452 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2663 ## 281 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8526 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7554352E-09 -3.2291139E-09 midg,1,midg; midg,igrid,midg 4.9015978E-09 -4.6870969E-09 1,midg,midg; igrid,midg,midg 1.8554195E-09 -6.6873879E-10 gauss-seidel spectral radius is 0.9851137 estimated iterations to convergence 67 setup time was (sec) 0.3900000 now iterating at: 19:38:42 rms-change max change #iterations 0.1044716 16.97191 at 10iterations 8.4290570E-03 1.307169 at 20iterations 6.9196883E-04 0.1027527 at 30iterations 5.6657103E-05 9.1857910E-03 at 40iterations 4.7144667E-06 6.9427490E-04 at 50iterations finished qdiffx linear iterations at : 19:38:44 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 4.7144667E-06 6.9427490E-04 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 19:38:45 3.372u 0.179s 0:03.83 92.4% 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 19:38:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2923 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: 1.766750 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): -4.351000 46.58900 ymin,ymax (A): -25.91800 34.53200 zmin,zma (A): -14.69100 37.85100 x,y,z range (A): 50.94000 60.45000 52.54200 scale (grids/A): 1.766750 object centre (A): 21.11900 4.306999 11.58000 number of atom coordinates read : 2923 total number of charged atoms : 2782 net assigned charge : 2.000025 assigned positive charge : 434.0884 centred at (gu) : 90.11066 91.08393 89.30431 assigned negative charge : -432.0894 centred at (gu) : 90.24345 91.58842 89.71947 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 73623 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25958 grid for indexing accessible points = 1.400000 m= 24575 mr = 50198 m= 3108 mr = 17645 m= 92 mr = 1612 m= 0 mr = 2 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 1319 time to turn everything in is 0.3500000 number of dielectric boundary points 31941 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 223 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 21687 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) : 0.5889165 object centre at (A) : 21.11900 4.306999 11.58000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.0092326E-03 -2.5672022E-02 midg,1,midg; midg,igrid,midg 1.5058749E-02 -1.0759544E-02 1,midg,midg; igrid,midg,midg 3.3849047E-03 -2.3522042E-04 gauss-seidel spectral radius is 0.9984549 estimated iterations to convergence 202 setup time was (sec) 0.5700000 now iterating at: 19:38:46 rms-change max change #iterations 3.890752 165.5687 at 10iterations 1.734087 60.44841 at 20iterations 0.7694651 25.20868 at 30iterations 0.3431661 11.11161 at 40iterations 0.1534065 4.961562 at 50iterations 6.8447247E-02 2.414260 at 60iterations 3.0590767E-02 1.063776 at 70iterations 1.3634090E-02 0.5096793 at 80iterations 6.0823383E-03 0.2088809 at 90iterations 2.7166780E-03 9.3780398E-02 at 100iterations 1.2100021E-03 3.7021637E-02 at 110iterations 5.4075132E-04 1.8347740E-02 at 120iterations finished qdiffx linear iterations at : 19:38:53 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 5.4075132E-04 1.8347740E-02 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 19:38:54 7.719u 0.201s 0:08.71 90.8% 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 19:38:54 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2923 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.650124 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): -4.351000 46.58900 ymin,ymax (A): -25.91800 34.53200 zmin,zma (A): -14.69100 37.85100 x,y,z range (A): 50.94000 60.45000 52.54200 scale (grids/A): 2.650124 object centre (A): 21.11900 4.306999 11.58000 number of atom coordinates read : 2923 total number of charged atoms : 2782 net assigned charge : 2.000025 assigned positive charge : 434.0884 centred at (gu) : 90.16578 91.62557 88.95623 assigned negative charge : -432.0894 centred at (gu) : 90.36510 92.38260 89.57912 start vw surface at 0.1000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 170659 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25958 grid for indexing accessible points = 1.400000 m= 82055 mr = 122394 m= 26789 mr = 66083 m= 5279 mr = 20934 m= 499 mr = 3501 m= 13 mr = 260 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 4490 time to turn everything in is 0.9100000 number of dielectric boundary points 72122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 22246 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) : 1.766750 object centre at (A) : 21.11900 4.306999 11.58000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0390627E-02 -0.3433009 midg,1,midg; midg,igrid,midg 0.1068420 -0.1828090 1,midg,midg; igrid,midg,midg 6.7170627E-02 -3.6962204E-02 gauss-seidel spectral radius is 0.9992193 estimated iterations to convergence 283 setup time was (sec) 1.150000 now iterating at: 19:38:55 rms-change max change #iterations 9.525790 291.1541 at 10iterations 5.529168 134.1098 at 20iterations 3.162862 65.50327 at 30iterations 1.805017 38.56021 at 40iterations 1.026644 22.15986 at 50iterations 0.5837903 11.94378 at 60iterations 0.3306516 6.472954 at 70iterations 0.1878019 3.693881 at 80iterations 0.1063356 2.051836 at 90iterations 6.0185932E-02 1.275642 at 100iterations 3.4046084E-02 0.7036076 at 110iterations 1.9228430E-02 0.3825235 at 120iterations 1.0884427E-02 0.1928425 at 130iterations 6.1638150E-03 0.1184769 at 140iterations 3.4786875E-03 6.5197945E-02 at 150iterations 1.9690569E-03 3.6628723E-02 at 160iterations 1.1124058E-03 2.0634651E-02 at 170iterations 6.2878127E-04 1.2720346E-02 at 180iterations finished qdiffx linear iterations at : 19:39:06 total time elapsed so far: 12.50000 # loops : 180 mean,max change (kT/e) : 6.2878127E-04 1.2720346E-02 energy calculations done at 12.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.63000 DelPhi exited at 19:39:07 12.636u 0.212s 0:13.20 97.2% 0+0k 0+0io 0pf+0w