Tue Oct 11 06:02:59 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+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 Tue Oct 11 2011 at 06:02:59 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2281 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: 0.7325856 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): 25.73800 72.09600 ymin,ymax (A): -18.55200 30.04300 zmin,zma (A): 3.939000 46.36400 x,y,z range (A): 46.35800 48.59500 42.42500 scale (grids/A): 0.7325856 object centre (A): 48.91700 5.745501 25.15150 number of atom coordinates read : 2281 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 89.10553 90.46965 90.27473 assigned negative charge : -311.0742 centred at (gu) : 89.23925 90.41437 90.35598 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7698 nv = 96 ne = 84 npr = 41770 no. pairs analyzed = 41770 no. exposed pairs = 2546 no. arc points = 17427 no. surface atoms = 867 nbur = 1414 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 593 mr = 4522 m= 3 mr = 140 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3632 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1553 ## 153 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8203 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5638075E-07 2.8057423E-08 midg,1,midg; midg,igrid,midg 4.5442157E-08 1.5593692E-07 1,midg,midg; igrid,midg,midg 2.4649921E-07 -1.4662754E-08 gauss-seidel spectral radius is 0.9902821 estimated iterations to convergence 82 setup time was (sec) 0.5300000 now iterating at: 06:03:00 rms-change max change #iterations 0.2267663 32.96989 at 10iterations 3.0303786E-02 3.587762 at 20iterations 4.2004846E-03 0.5055099 at 30iterations 6.7852769E-04 8.9719772E-02 at 40iterations 1.6690587E-04 2.0570755E-02 at 50iterations finished qdiffx linear iterations at : 06:03:03 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 1.6690587E-04 2.0570755E-02 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 06:03:03 3.546u 0.192s 0:04.19 89.0% 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 06:03:03 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2281 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: 2.197757 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): 25.73800 72.09600 ymin,ymax (A): -18.55200 30.04300 zmin,zma (A): 3.939000 46.36400 x,y,z range (A): 46.35800 48.59500 42.42500 scale (grids/A): 2.197757 object centre (A): 48.91700 5.745501 25.15150 number of atom coordinates read : 2281 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 87.31654 91.40893 90.82442 assigned negative charge : -311.0742 centred at (gu) : 87.71775 91.24326 91.06815 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 81177 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17427 grid for indexing accessible points = 1.400000 m= 34234 mr = 58228 m= 7342 mr = 26611 m= 818 mr = 5124 m= 33 mr = 481 m= 0 mr = 9 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 33151 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 43 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 15598 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) : 0.7325856 object centre at (A) : 48.91700 5.745501 25.15150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7122440E-02 3.1892385E-02 midg,1,midg; midg,igrid,midg 5.0948367E-02 3.7082870E-02 1,midg,midg; igrid,midg,midg 5.2834265E-02 -5.6009274E-02 gauss-seidel spectral radius is 0.9988997 estimated iterations to convergence 239 setup time was (sec) 0.9600000 now iterating at: 06:03:04 rms-change max change #iterations 4.910985 203.8950 at 10iterations 2.470034 81.07284 at 20iterations 1.256797 37.63181 at 30iterations 0.6348145 19.76580 at 40iterations 0.3221210 9.079830 at 50iterations 0.1639475 4.742493 at 60iterations 8.2885623E-02 2.179311 at 70iterations 4.2184927E-02 1.176048 at 80iterations 2.1358741E-02 0.6127548 at 90iterations 1.0946174E-02 0.3046474 at 100iterations 5.5935802E-03 0.1751957 at 110iterations 2.9039856E-03 8.2920074E-02 at 120iterations finished qdiffx linear iterations at : 06:03:12 total time elapsed so far: 8.320000 # loops : 120 mean,max change (kT/e) : 2.9039856E-03 8.2920074E-02 energy calculations done at 8.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.790000 DelPhi exited at 06:03:15 8.789u 0.569s 0:11.68 79.9% 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 06:03:15 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2281 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: 3.296635 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): 25.73800 72.09600 ymin,ymax (A): -18.55200 30.04300 zmin,zma (A): 3.939000 46.36400 x,y,z range (A): 46.35800 48.59500 42.42500 scale (grids/A): 3.296635 object centre (A): 48.91700 5.745501 25.15150 number of atom coordinates read : 2281 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 85.97475 92.11336 91.23656 assigned negative charge : -311.0742 centred at (gu) : 86.57668 91.86484 91.60239 start vw surface at 0.1700000 fill in re-entrant regions at 0.9400000 boundary points on vw surface= 186751 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17427 grid for indexing accessible points = 1.400000 m= 105155 mr = 139745 m= 45516 mr = 88475 m= 14269 mr = 38190 m= 3299 mr = 11508 m= 489 mr = 2482 m= 29 mr = 341 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.090000 number of dielectric boundary points 74754 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.230000 number of grid points assigned charge 15688 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) : 2.197757 object centre at (A) : 48.91700 5.745501 25.15150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1225728 0.2844655 midg,1,midg; midg,igrid,midg 0.3746863 0.2039810 1,midg,midg; igrid,midg,midg 0.5001945 -0.6497636 gauss-seidel spectral radius is 0.9993140 estimated iterations to convergence 301 setup time was (sec) 2.450000 now iterating at: 06:03:18 rms-change max change #iterations 10.73015 340.8733 at 10iterations 6.390114 133.5552 at 20iterations 3.797091 73.26244 at 30iterations 2.261562 41.83165 at 40iterations 1.341790 22.19890 at 50iterations 0.7935616 13.40727 at 60iterations 0.4696027 9.084499 at 70iterations 0.2772090 4.793918 at 80iterations 0.1636552 2.660507 at 90iterations 9.6620917E-02 1.699192 at 100iterations 5.7126768E-02 1.109055 at 110iterations 3.3836238E-02 0.5458946 at 120iterations 2.0143954E-02 0.3360767 at 130iterations 1.2077810E-02 0.2145958 at 140iterations 7.3606460E-03 0.1315269 at 150iterations 4.6091056E-03 8.7903976E-02 at 160iterations 3.0061654E-03 5.4367065E-02 at 170iterations 2.0723322E-03 3.7254333E-02 at 180iterations finished qdiffx linear iterations at : 06:03:31 total time elapsed so far: 14.73000 # loops : 180 mean,max change (kT/e) : 2.0723322E-03 3.7254333E-02 energy calculations done at 14.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.91000 DelPhi exited at 06:03:31 14.915u 0.233s 0:15.74 96.1% 0+0k 0+0io 0pf+0w