Mon Oct 10 17:15:46 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+sph2.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 = amb2.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 17:15:47 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2848 !!! WARNING: GLM 775 has a net charge of -0.0940 !!! WARNING: GLM 817 has a net charge of -0.0940 !!! WARNING: GLU 858 has a net charge of -2.0000 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: 0.5831668 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): -15.01800 46.02800 ymin,ymax (A): -31.51300 27.02800 zmin,zma (A): -7.984000 44.02500 x,y,z range (A): 61.04600 58.54100 52.00900 scale (grids/A): 0.5831668 object centre (A): 15.50500 -2.242500 18.02050 number of atom coordinates read : 2848 total number of charged atoms : 2696 net assigned charge : -1.687989 assigned positive charge : 427.3004 centred at (gu) : 87.90835 90.23076 90.34785 assigned negative charge : -428.9894 centred at (gu) : 88.04449 90.21074 90.35224 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6243 nv = 96 ne = 84 npr = 59157 no. pairs analyzed = 59157 no. exposed pairs = 3494 no. arc points = 24527 no. surface atoms = 1175 nbur = 1673 mkacc time = 0.1600000 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= 313 mr = 3322 m= 0 mr = 14 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3300000 number of dielectric boundary points 3220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2495 ## 285 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8028 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.5147643E-10 -6.3508637E-10 midg,1,midg; midg,igrid,midg -9.0464497E-10 -1.3779093E-11 1,midg,midg; igrid,midg,midg 4.4171395E-09 -2.2917310E-09 gauss-seidel spectral radius is 0.9848087 estimated iterations to convergence 67 setup time was (sec) 0.6600000 now iterating at: 17:15:48 rms-change max change #iterations 9.9695563E-02 16.53947 at 10iterations 7.9066213E-03 1.238268 at 20iterations 6.2754226E-04 9.7993851E-02 at 30iterations 5.6399866E-05 9.0551376E-03 at 40iterations 6.3174371E-06 9.9468231E-04 at 50iterations finished qdiffx linear iterations at : 17:15:52 total time elapsed so far: 4.870000 # loops : 50 mean,max change (kT/e) : 6.3174371E-06 9.9468231E-04 energy calculations done at 4.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.040000 DelPhi exited at 17:15:52 5.044u 0.449s 0:05.83 93.9% 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 Mon Oct 10 2011 at 17:15:52 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2848 !!! WARNING: GLM 775 has a net charge of -0.0940 !!! WARNING: GLM 817 has a net charge of -0.0940 !!! WARNING: GLU 858 has a net charge of -2.0000 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: 1.749500 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): -15.01800 46.02800 ymin,ymax (A): -31.51300 27.02800 zmin,zma (A): -7.984000 44.02500 x,y,z range (A): 61.04600 58.54100 52.00900 scale (grids/A): 1.749500 object centre (A): 15.50500 -2.242500 18.02050 number of atom coordinates read : 2848 total number of charged atoms : 2696 net assigned charge : -1.687989 assigned positive charge : 427.3004 centred at (gu) : 83.72458 90.69155 91.04303 assigned negative charge : -428.9894 centred at (gu) : 84.13304 90.63190 91.05663 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 68951 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24527 grid for indexing accessible points = 1.400000 m= 21782 mr = 47093 m= 2683 mr = 15282 m= 100 mr = 1507 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 235 time to turn everything in is 0.5800000 number of dielectric boundary points 29605 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 218 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 20909 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) : 0.5831668 object centre at (A) : 15.50500 -2.242500 18.02050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6475111E-03 -3.5155874E-05 midg,1,midg; midg,igrid,midg 1.5063252E-02 8.5303793E-03 1,midg,midg; igrid,midg,midg 2.6223829E-02 -1.5609386E-02 gauss-seidel spectral radius is 0.9984094 estimated iterations to convergence 199 setup time was (sec) 0.9000000 now iterating at: 17:15:54 rms-change max change #iterations 3.805822 168.4415 at 10iterations 1.674369 65.95195 at 20iterations 0.7398140 25.16240 at 30iterations 0.3254554 11.61479 at 40iterations 0.1432638 4.987511 at 50iterations 6.3700132E-02 2.280634 at 60iterations 2.7992597E-02 0.8997726 at 70iterations 1.2386851E-02 0.4149685 at 80iterations 5.4674810E-03 0.1786366 at 90iterations 2.4037389E-03 8.3625793E-02 at 100iterations 1.0624954E-03 3.5526276E-02 at 110iterations 4.6856079E-04 1.6139984E-02 at 120iterations finished qdiffx linear iterations at : 17:16:05 total time elapsed so far: 11.56000 # loops : 120 mean,max change (kT/e) : 4.6856079E-04 1.6139984E-02 energy calculations done at 11.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.73000 DelPhi exited at 17:16:05 11.739u 0.513s 0:12.63 96.9% 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 Mon Oct 10 2011 at 17:16:05 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2848 !!! WARNING: GLM 775 has a net charge of -0.0940 !!! WARNING: GLM 817 has a net charge of -0.0940 !!! WARNING: GLU 858 has a net charge of -2.0000 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: 2.624251 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): -15.01800 46.02800 ymin,ymax (A): -31.51300 27.02800 zmin,zma (A): -7.984000 44.02500 x,y,z range (A): 61.04600 58.54100 52.00900 scale (grids/A): 2.624251 object centre (A): 15.50500 -2.242500 18.02050 number of atom coordinates read : 2848 total number of charged atoms : 2696 net assigned charge : -1.687989 assigned positive charge : 427.3004 centred at (gu) : 80.58669 91.03715 91.56441 assigned negative charge : -428.9894 centred at (gu) : 81.19949 90.94762 91.58501 start vw surface at 0.1300000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 159957 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24527 grid for indexing accessible points = 1.400000 m= 73621 mr = 115094 m= 23374 mr = 58495 m= 4475 mr = 18099 m= 466 mr = 3145 m= 17 mr = 295 m= 0 mr = 5 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 760 time to turn everything in is 1.510000 number of dielectric boundary points 66777 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 21562 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) : 1.749500 object centre at (A) : 15.50500 -2.242500 18.02050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2944596E-02 4.5798708E-02 midg,1,midg; midg,igrid,midg 0.1759734 0.1565003 1,midg,midg; igrid,midg,midg 0.6780862 -0.2298230 gauss-seidel spectral radius is 0.9992040 estimated iterations to convergence 280 setup time was (sec) 1.910000 now iterating at: 17:16:08 rms-change max change #iterations 9.368905 313.8332 at 10iterations 5.367596 135.3517 at 20iterations 3.060751 73.34071 at 30iterations 1.737686 35.75057 at 40iterations 0.9864153 23.23181 at 50iterations 0.5564121 11.15987 at 60iterations 0.3152101 6.718025 at 70iterations 0.1776412 3.560822 at 80iterations 0.1001865 2.217327 at 90iterations 5.6420043E-02 1.210831 at 100iterations 3.1833265E-02 0.6321411 at 110iterations 1.7921578E-02 0.3282809 at 120iterations 1.0092679E-02 0.1979618 at 130iterations 5.6658098E-03 0.1105371 at 140iterations 3.2009117E-03 6.2613964E-02 at 150iterations 1.7996242E-03 3.8406372E-02 at 160iterations 1.0127797E-03 2.0402908E-02 at 170iterations 5.7243765E-04 1.0510445E-02 at 180iterations finished qdiffx linear iterations at : 17:16:25 total time elapsed so far: 19.64000 # loops : 180 mean,max change (kT/e) : 5.7243765E-04 1.0510445E-02 energy calculations done at 19.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.81000 DelPhi exited at 17:16:26 19.811u 0.504s 0:20.77 97.7% 0+0k 0+0io 0pf+0w