Mon Oct 10 14:24:44 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 14:24:44 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2576 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: 0.6110119 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): -7.914000 44.05300 ymin,ymax (A): 12.97400 71.23800 zmin,zma (A): 55.66400 107.6440 x,y,z range (A): 51.96700 58.26400 51.98000 scale (grids/A): 0.6110119 object centre (A): 18.06950 42.10600 81.65400 number of atom coordinates read : 2576 total number of charged atoms : 2417 net assigned charge : -1.999991 assigned positive charge : 379.3019 centred at (gu) : 90.09074 90.83422 89.64139 assigned negative charge : -381.3025 centred at (gu) : 89.85101 90.71688 89.66421 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6453 nv = 96 ne = 84 npr = 51434 no. pairs analyzed = 51434 no. exposed pairs = 3548 no. arc points = 25164 no. surface atoms = 1190 nbur = 1386 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 316 mr = 3206 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3550 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2452 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7881 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3497994E-10 -2.2327165E-09 midg,1,midg; midg,igrid,midg -5.9955014E-09 5.5000329E-09 1,midg,midg; igrid,midg,midg -1.3342865E-08 1.0642405E-08 gauss-seidel spectral radius is 0.9861370 estimated iterations to convergence 70 setup time was (sec) 0.5900000 now iterating at: 14:24:45 rms-change max change #iterations 0.1100441 15.82222 at 10iterations 9.6948501E-03 1.725683 at 20iterations 8.5463107E-04 0.1434746 at 30iterations 7.7092744E-05 1.1526108E-02 at 40iterations 6.9409730E-06 9.9182129E-04 at 50iterations finished qdiffx linear iterations at : 14:24:48 total time elapsed so far: 3.480000 # loops : 50 mean,max change (kT/e) : 6.9409730E-06 9.9182129E-04 energy calculations done at 3.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.670000 DelPhi exited at 14:24:48 3.676u 0.187s 0:04.24 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 14:24:48 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2576 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.833036 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): -7.914000 44.05300 ymin,ymax (A): 12.97400 71.23800 zmin,zma (A): 55.66400 107.6440 x,y,z range (A): 51.96700 58.26400 51.98000 scale (grids/A): 1.833036 object centre (A): 18.06950 42.10600 81.65400 number of atom coordinates read : 2576 total number of charged atoms : 2417 net assigned charge : -1.999991 assigned positive charge : 379.3019 centred at (gu) : 90.27161 92.50230 88.92374 assigned negative charge : -381.3025 centred at (gu) : 89.55281 92.15038 88.99233 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 69404 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25164 grid for indexing accessible points = 1.400000 m= 22668 mr = 45523 m= 2969 mr = 15485 m= 141 mr = 1467 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 32683 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 186 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 18943 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) : 0.6110119 object centre at (A) : 18.06950 42.10600 81.65400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2478933E-02 2.3675573E-03 midg,1,midg; midg,igrid,midg -6.0117310E-03 4.4856407E-03 1,midg,midg; igrid,midg,midg -3.4250163E-02 8.4847659E-03 gauss-seidel spectral radius is 0.9985340 estimated iterations to convergence 207 setup time was (sec) 0.9000000 now iterating at: 14:24:49 rms-change max change #iterations 3.891795 167.9520 at 10iterations 1.758003 64.85809 at 20iterations 0.7991468 27.66800 at 30iterations 0.3636203 12.61496 at 40iterations 0.1650769 5.748825 at 50iterations 7.5157881E-02 2.533373 at 60iterations 3.4199938E-02 1.244738 at 70iterations 1.5535001E-02 0.5278130 at 80iterations 7.0835724E-03 0.2763567 at 90iterations 3.2169605E-03 0.1191616 at 100iterations 1.4604734E-03 5.4164886E-02 at 110iterations 6.6874200E-04 2.4349213E-02 at 120iterations finished qdiffx linear iterations at : 14:24:56 total time elapsed so far: 7.990000 # loops : 120 mean,max change (kT/e) : 6.6874200E-04 2.4349213E-02 energy calculations done at 7.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.180000 DelPhi exited at 14:24:57 8.179u 0.211s 0:09.10 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 Mon Oct 10 2011 at 14:24:57 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2576 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.749554 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): -7.914000 44.05300 ymin,ymax (A): 12.97400 71.23800 zmin,zma (A): 55.66400 107.6440 x,y,z range (A): 51.96700 58.26400 51.98000 scale (grids/A): 2.749554 object centre (A): 18.06950 42.10600 81.65400 number of atom coordinates read : 2576 total number of charged atoms : 2417 net assigned charge : -1.999991 assigned positive charge : 379.3019 centred at (gu) : 90.40741 93.75326 88.38540 assigned negative charge : -381.3025 centred at (gu) : 89.32903 93.22546 88.48853 start vw surface at 0.1700000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 160663 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25164 grid for indexing accessible points = 1.400000 m= 75359 mr = 111564 m= 24607 mr = 58856 m= 4851 mr = 18500 m= 545 mr = 3113 m= 41 mr = 269 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.7600001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.340000 number of dielectric boundary points 73750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 19331 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) : 1.833036 object centre at (A) : 18.06950 42.10600 81.65400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2580850 6.0796846E-02 midg,1,midg; midg,igrid,midg -4.1975413E-02 -5.0950609E-02 1,midg,midg; igrid,midg,midg -0.3577717 3.6907848E-02 gauss-seidel spectral radius is 0.9992395 estimated iterations to convergence 286 setup time was (sec) 1.670000 now iterating at: 14:24:59 rms-change max change #iterations 9.454916 325.5030 at 10iterations 5.540712 157.3077 at 20iterations 3.222358 74.77013 at 30iterations 1.862636 41.92745 at 40iterations 1.075185 23.36093 at 50iterations 0.6182320 13.36166 at 60iterations 0.3542511 7.778727 at 70iterations 0.2030523 4.364698 at 80iterations 0.1162340 2.366299 at 90iterations 6.6399053E-02 1.308149 at 100iterations 3.7980691E-02 0.8636537 at 110iterations 2.1655032E-02 0.4383831 at 120iterations 1.2372581E-02 0.2484174 at 130iterations 7.0565110E-03 0.1526467 at 140iterations 4.0285978E-03 7.4119568E-02 at 150iterations 2.2973483E-03 4.7971249E-02 at 160iterations 1.3097922E-03 2.6838303E-02 at 170iterations 7.4739550E-04 1.5450954E-02 at 180iterations finished qdiffx linear iterations at : 14:25:10 total time elapsed so far: 12.77000 # loops : 180 mean,max change (kT/e) : 7.4739550E-04 1.5450954E-02 energy calculations done at 12.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.96000 DelPhi exited at 14:25:11 12.961u 0.248s 0:13.76 95.9% 0+0k 0+0io 0pf+0w