Mon Oct 10 10:24:18 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 10:24:18 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 = 2665 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: 0.5790030 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): 18.94200 80.42700 ymin,ymax (A): 33.71100 88.81300 zmin,zma (A): -1.291000 50.97700 x,y,z range (A): 61.48500 55.10201 52.26800 scale (grids/A): 0.5790030 object centre (A): 49.68450 61.26200 24.84300 number of atom coordinates read : 2665 total number of charged atoms : 2521 net assigned charge : 12.00002 assigned positive charge : 390.2872 centred at (gu) : 87.99586 88.50855 86.80551 assigned negative charge : -378.2876 centred at (gu) : 87.92410 88.51070 86.64470 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6101 nv = 96 ne = 84 npr = 50983 no. pairs analyzed = 50983 no. exposed pairs = 4005 no. arc points = 29164 no. surface atoms = 1325 nbur = 1340 mkacc time = 0.1400000 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 = 1.484000 m= 283 mr = 2749 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.3200000 number of dielectric boundary points 3625 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2817 ## 317 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7630 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.4037571E-10 2.6058486E-09 midg,1,midg; midg,igrid,midg 3.7372017E-09 1.8416439E-09 1,midg,midg; igrid,midg,midg 2.0670492E-09 2.4528006E-09 gauss-seidel spectral radius is 0.9845958 estimated iterations to convergence 66 setup time was (sec) 0.6300000 now iterating at: 10:24:19 rms-change max change #iterations 8.9342721E-02 14.41240 at 10iterations 6.9740275E-03 1.158819 at 20iterations 5.3350592E-04 8.1504822E-02 at 30iterations 5.0449333E-05 8.3022118E-03 at 40iterations 7.1083391E-06 8.0299377E-04 at 50iterations finished qdiffx linear iterations at : 10:24:23 total time elapsed so far: 4.700000 # loops : 50 mean,max change (kT/e) : 7.1083391E-06 8.0299377E-04 energy calculations done at 4.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.870000 DelPhi exited at 10:24:23 4.874u 0.384s 0:05.55 94.5% 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 Mon Oct 10 2011 at 10:24:23 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 = 2665 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: 1.737009 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): 18.94200 80.42700 ymin,ymax (A): 33.71100 88.81300 zmin,zma (A): -1.291000 50.97700 x,y,z range (A): 61.48500 55.10201 52.26800 scale (grids/A): 1.737009 object centre (A): 49.68450 61.26200 24.84300 number of atom coordinates read : 2665 total number of charged atoms : 2521 net assigned charge : 12.00002 assigned positive charge : 390.2872 centred at (gu) : 83.98717 85.52521 80.41621 assigned negative charge : -378.2876 centred at (gu) : 83.77213 85.53200 79.93388 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 65935 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29164 grid for indexing accessible points = 1.400000 m= 20170 mr = 40908 m= 2404 mr = 12733 m= 97 mr = 1076 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 33884 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 257 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 19523 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) : 0.5790030 object centre at (A) : 49.68450 61.26200 24.84300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7617187E-03 9.4483932E-03 midg,1,midg; midg,igrid,midg 2.3921976E-02 1.6669935E-02 1,midg,midg; igrid,midg,midg 2.9544255E-02 1.7754048E-02 gauss-seidel spectral radius is 0.9983823 estimated iterations to convergence 197 setup time was (sec) 0.9100000 now iterating at: 10:24:25 rms-change max change #iterations 3.468345 153.2109 at 10iterations 1.507512 60.85648 at 20iterations 0.6538978 24.60757 at 30iterations 0.2853062 10.23446 at 40iterations 0.1245592 4.694714 at 50iterations 5.4323703E-02 1.880745 at 60iterations 2.3707494E-02 0.8911125 at 70iterations 1.0350218E-02 0.3495243 at 80iterations 4.5139911E-03 0.1630840 at 90iterations 1.9697642E-03 7.1055412E-02 at 100iterations 8.6407008E-04 3.1326294E-02 at 110iterations 3.7830372E-04 1.4076233E-02 at 120iterations finished qdiffx linear iterations at : 10:24:35 total time elapsed so far: 11.70000 # loops : 120 mean,max change (kT/e) : 3.7830372E-04 1.4076233E-02 energy calculations done at 11.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.87000 DelPhi exited at 10:24:36 11.878u 0.448s 0:12.81 96.0% 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 10:24:36 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 = 2665 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: 2.605514 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): 18.94200 80.42700 ymin,ymax (A): 33.71100 88.81300 zmin,zma (A): -1.291000 50.97700 x,y,z range (A): 61.48500 55.10201 52.26800 scale (grids/A): 2.605514 object centre (A): 49.68450 61.26200 24.84300 number of atom coordinates read : 2665 total number of charged atoms : 2521 net assigned charge : 12.00002 assigned positive charge : 390.2872 centred at (gu) : 80.98055 83.28778 75.62424 assigned negative charge : -378.2876 centred at (gu) : 80.65819 83.29800 74.90082 start vw surface at 0.1300000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 152480 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29164 grid for indexing accessible points = 1.400000 m= 67853 mr = 100865 m= 20547 mr = 50906 m= 3748 mr = 14471 m= 331 mr = 2171 m= 6 mr = 148 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.410000 number of dielectric boundary points 76404 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 20161 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) : 1.737009 object centre at (A) : 49.68450 61.26200 24.84300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0343390E-02 8.5882582E-02 midg,1,midg; midg,igrid,midg 0.2735640 0.2089308 1,midg,midg; igrid,midg,midg 0.4106388 0.4983589 gauss-seidel spectral radius is 0.9992006 estimated iterations to convergence 279 setup time was (sec) 1.780000 now iterating at: 10:24:38 rms-change max change #iterations 8.964246 283.3641 at 10iterations 5.275454 169.3495 at 20iterations 3.056746 83.76294 at 30iterations 1.761397 54.95929 at 40iterations 1.005152 26.43515 at 50iterations 0.5727661 14.27746 at 60iterations 0.3251699 8.044188 at 70iterations 0.1839400 4.354271 at 80iterations 0.1041205 2.553164 at 90iterations 5.8869693E-02 1.315218 at 100iterations 3.3126757E-02 0.7256694 at 110iterations 1.8701740E-02 0.3961143 at 120iterations 1.0498333E-02 0.2075891 at 130iterations 5.9117470E-03 0.1256981 at 140iterations 3.3281441E-03 7.8534126E-02 at 150iterations 1.8750963E-03 3.8695335E-02 at 160iterations 1.0528348E-03 2.1438599E-02 at 170iterations 5.9189519E-04 1.1970997E-02 at 180iterations finished qdiffx linear iterations at : 10:24:57 total time elapsed so far: 20.28000 # loops : 180 mean,max change (kT/e) : 5.9189519E-04 1.1970997E-02 energy calculations done at 20.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.44000 DelPhi exited at 10:24:57 20.447u 0.476s 0:21.25 98.4% 0+0k 0+0io 0pf+0w