Tue Oct 11 05:49:01 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 05:49:01 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 = 2290 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: 0.7408024 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): 25.63100 72.61900 ymin,ymax (A): -18.38900 29.66700 zmin,zma (A): 4.004000 45.95000 x,y,z range (A): 46.98801 48.05600 41.94600 scale (grids/A): 0.7408024 object centre (A): 49.12500 5.639000 24.97700 number of atom coordinates read : 2290 total number of charged atoms : 1969 net assigned charge : 6.500009 assigned positive charge : 319.1440 centred at (gu) : 89.00467 90.54456 90.26672 assigned negative charge : -312.6442 centred at (gu) : 89.13279 90.48396 90.34825 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7917 nv = 96 ne = 84 npr = 42142 no. pairs analyzed = 42142 no. exposed pairs = 2562 no. arc points = 17397 no. surface atoms = 880 nbur = 1410 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 588 mr = 4637 m= 2 mr = 110 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3760 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1571 ## 146 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8348 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8715077E-07 3.3501589E-08 midg,1,midg; midg,igrid,midg 4.8977647E-08 1.9435018E-07 1,midg,midg; igrid,midg,midg 2.9232234E-07 -1.1851175E-08 gauss-seidel spectral radius is 0.9904952 estimated iterations to convergence 83 setup time was (sec) 0.3700000 now iterating at: 05:49:01 rms-change max change #iterations 0.2449341 31.09696 at 10iterations 3.3131294E-02 3.933487 at 20iterations 4.7430005E-03 0.6194458 at 30iterations 8.3385507E-04 0.1041870 at 40iterations 2.1805978E-04 2.5335312E-02 at 50iterations finished qdiffx linear iterations at : 05:49:04 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 2.1805978E-04 2.5335312E-02 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 05:49:05 3.393u 0.161s 0:03.94 90.1% 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 05:49:05 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 = 2290 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: 2.222407 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): 25.63100 72.61900 ymin,ymax (A): -18.38900 29.66700 zmin,zma (A): 4.004000 45.95000 x,y,z range (A): 46.98801 48.05600 41.94600 scale (grids/A): 2.222407 object centre (A): 49.12500 5.639000 24.97700 number of atom coordinates read : 2290 total number of charged atoms : 1969 net assigned charge : 6.500009 assigned positive charge : 319.1440 centred at (gu) : 87.01407 91.63367 90.80013 assigned negative charge : -312.6442 centred at (gu) : 87.39848 91.45219 91.04496 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 83057 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17397 grid for indexing accessible points = 1.400000 m= 34990 mr = 59579 m= 7427 mr = 26931 m= 824 mr = 5140 m= 30 mr = 421 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 34258 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 44 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 15672 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) : 0.7408024 object centre at (A) : 49.12500 5.639000 24.97700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4872471E-02 3.5441656E-02 midg,1,midg; midg,igrid,midg 5.2308742E-02 4.4277731E-02 1,midg,midg; igrid,midg,midg 5.9826378E-02 -5.1322661E-02 gauss-seidel spectral radius is 0.9989203 estimated iterations to convergence 241 setup time was (sec) 0.6600000 now iterating at: 05:49:05 rms-change max change #iterations 5.001585 219.7740 at 10iterations 2.542983 80.34644 at 20iterations 1.299703 41.33521 at 30iterations 0.6627890 20.04113 at 40iterations 0.3387780 9.273211 at 50iterations 0.1730288 4.768745 at 60iterations 8.8322818E-02 2.310504 at 70iterations 4.5156192E-02 1.229279 at 80iterations 2.3197681E-02 0.7996889 at 90iterations 1.1951037E-02 0.3133707 at 100iterations 6.1910227E-03 0.2015076 at 110iterations 3.2499607E-03 9.0911865E-02 at 120iterations finished qdiffx linear iterations at : 05:49:13 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 3.2499607E-03 9.0911865E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.020000 DelPhi exited at 05:49:13 8.020u 0.202s 0:08.66 94.9% 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 05:49:13 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 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: 3.333611 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): 25.63100 72.61900 ymin,ymax (A): -18.38900 29.66700 zmin,zma (A): 4.004000 45.95000 x,y,z range (A): 46.98801 48.05600 41.94600 scale (grids/A): 3.333611 object centre (A): 49.12500 5.639000 24.97700 number of atom coordinates read : 2290 total number of charged atoms : 1969 net assigned charge : 6.500009 assigned positive charge : 319.1440 centred at (gu) : 85.52110 92.45049 91.20022 assigned negative charge : -312.6442 centred at (gu) : 86.09773 92.17828 91.56747 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 190953 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17397 grid for indexing accessible points = 1.400000 m= 107050 mr = 142687 m= 46319 mr = 90109 m= 14499 mr = 38562 m= 3364 mr = 11423 m= 482 mr = 2444 m= 43 mr = 326 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.6999999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.330000 number of dielectric boundary points 77137 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 15748 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) : 2.222407 object centre at (A) : 49.12500 5.639000 24.97700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1116613 0.2798713 midg,1,midg; midg,igrid,midg 0.4567385 0.3000270 1,midg,midg; igrid,midg,midg 0.5469799 -0.5942459 gauss-seidel spectral radius is 0.9993197 estimated iterations to convergence 302 setup time was (sec) 1.570000 now iterating at: 05:49:15 rms-change max change #iterations 10.91156 266.0716 at 10iterations 6.524268 143.1242 at 20iterations 3.895941 87.48721 at 30iterations 2.318035 43.23286 at 40iterations 1.382720 26.86399 at 50iterations 0.8204962 15.48420 at 60iterations 0.4858620 8.147400 at 70iterations 0.2875532 5.399139 at 80iterations 0.1701854 2.935558 at 90iterations 0.1006528 1.640987 at 100iterations 5.9647437E-02 0.9873505 at 110iterations 3.5402507E-02 0.5692570 at 120iterations 2.1157889E-02 0.3520279 at 130iterations 1.2749144E-02 0.2165527 at 140iterations 7.8505641E-03 0.1325150 at 150iterations 5.0067711E-03 8.6322784E-02 at 160iterations 3.3380771E-03 5.4431915E-02 at 170iterations 2.3712595E-03 3.7918091E-02 at 180iterations finished qdiffx linear iterations at : 05:49:27 total time elapsed so far: 13.04000 # loops : 180 mean,max change (kT/e) : 2.3712595E-03 3.7918091E-02 energy calculations done at 13.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.18000 DelPhi exited at 05:49:27 13.180u 0.224s 0:13.73 97.5% 0+0k 0+0io 0pf+0w