Sat Oct 8 11:39:23 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 Sat Oct 8 2011 at 11:39:23 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4256 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5258028 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): -1.757000 65.94900 ymin,ymax (A): -10.24800 37.84100 zmin,zma (A): -19.70200 43.98100 x,y,z range (A): 67.70599 48.08900 63.68300 scale (grids/A): 0.5258028 object centre (A): 32.09600 13.79650 12.13950 number of atom coordinates read : 4256 total number of charged atoms : 4101 net assigned charge : -7.499957 assigned positive charge : 639.8351 centred at (gu) : 87.76403 89.82531 90.44973 assigned negative charge : -647.3375 centred at (gu) : 87.82343 89.90822 90.48689 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6734 nv = 96 ne = 84 npr = 95107 no. pairs analyzed = 95107 no. exposed pairs = 4414 no. arc points = 30255 no. surface atoms = 1511 nbur = 2745 mkacc time = 0.2300000 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 = 1.624000 m= 240 mr = 3774 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 86 time to turn everything in is 0.4500000 number of dielectric boundary points 3189 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3071 ## 428 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 9539 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3889652E-11 -4.2022977E-10 midg,1,midg; midg,igrid,midg 1.5703250E-10 -5.5353772E-10 1,midg,midg; igrid,midg,midg 9.6835290E-11 -2.6953670E-10 gauss-seidel spectral radius is 0.9814347 estimated iterations to convergence 61 setup time was (sec) 0.7100000 now iterating at: 11:39:24 rms-change max change #iterations 7.1542919E-02 9.491091 at 10iterations 4.6099881E-03 0.7897091 at 20iterations 3.6836325E-04 6.3397408E-02 at 30iterations 5.2267234E-05 8.8424683E-03 at 40iterations 9.7085413E-06 1.6860962E-03 at 50iterations finished qdiffx linear iterations at : 11:39:29 total time elapsed so far: 4.970000 # loops : 50 mean,max change (kT/e) : 9.7085413E-06 1.6860962E-03 energy calculations done at 4.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.150000 DelPhi exited at 11:39:29 5.151u 0.417s 0:05.90 94.2% 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 Sat Oct 8 2011 at 11:39:29 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 = 4256 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.577408 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): -1.757000 65.94900 ymin,ymax (A): -10.24800 37.84100 zmin,zma (A): -19.70200 43.98100 x,y,z range (A): 67.70599 48.08900 63.68300 scale (grids/A): 1.577408 object centre (A): 32.09600 13.79650 12.13950 number of atom coordinates read : 4256 total number of charged atoms : 4101 net assigned charge : -7.499957 assigned positive charge : 639.8351 centred at (gu) : 83.29092 89.47486 91.34789 assigned negative charge : -647.3375 centred at (gu) : 83.46957 89.72396 91.46008 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 77464 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30255 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 20889 mr = 55620 m= 1819 mr = 14167 m= 48 mr = 841 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 5707 time to turn everything in is 0.6200000 number of dielectric boundary points 29592 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 360 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 31180 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) : 0.5258028 object centre at (A) : 32.09600 13.79650 12.13950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0203317E-02 -1.1844368E-02 midg,1,midg; midg,igrid,midg -4.2844638E-03 -1.1912483E-02 1,midg,midg; igrid,midg,midg 1.9611113E-02 -7.5603225E-03 gauss-seidel spectral radius is 0.9981371 estimated iterations to convergence 184 setup time was (sec) 0.9800000 now iterating at: 11:39:30 rms-change max change #iterations 3.764833 161.1258 at 10iterations 1.550263 46.51865 at 20iterations 0.6406399 22.10255 at 30iterations 0.2642387 10.21801 at 40iterations 0.1093663 3.833115 at 50iterations 4.5171537E-02 1.508807 at 60iterations 1.8676763E-02 0.5792227 at 70iterations 7.7536618E-03 0.2527485 at 80iterations 3.2134661E-03 0.1026649 at 90iterations 1.3350132E-03 4.5789242E-02 at 100iterations 5.5300782E-04 1.8680573E-02 at 110iterations 2.3087545E-04 8.4686279E-03 at 120iterations finished qdiffx linear iterations at : 11:39:42 total time elapsed so far: 12.39000 # loops : 120 mean,max change (kT/e) : 2.3087545E-04 8.4686279E-03 energy calculations done at 12.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.57000 DelPhi exited at 11:39:42 12.579u 0.455s 0:13.35 97.5% 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 Sat Oct 8 2011 at 11:39:42 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 = 4256 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.366112 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): -1.757000 65.94900 ymin,ymax (A): -10.24800 37.84100 zmin,zma (A): -19.70200 43.98100 x,y,z range (A): 67.70599 48.08900 63.68300 scale (grids/A): 2.366112 object centre (A): 32.09600 13.79650 12.13950 number of atom coordinates read : 4256 total number of charged atoms : 4101 net assigned charge : -7.499957 assigned positive charge : 639.8351 centred at (gu) : 79.93613 89.21204 92.02158 assigned negative charge : -647.3375 centred at (gu) : 80.20432 89.58579 92.18981 start vw surface at 0.1500000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 181550 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30255 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 76367 mr = 136457 m= 18493 mr = 60553 m= 2700 mr = 13707 m= 124 mr = 1742 m= 0 mr = 35 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 19360 time to turn everything in is 1.550000 number of dielectric boundary points 66740 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 32740 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) : 1.577408 object centre at (A) : 32.09600 13.79650 12.13950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2583363 -0.2368619 midg,1,midg; midg,igrid,midg -8.7622344E-02 -0.1708118 1,midg,midg; igrid,midg,midg 0.5455702 -0.3973280 gauss-seidel spectral radius is 0.9991350 estimated iterations to convergence 269 setup time was (sec) 1.900000 now iterating at: 11:39:45 rms-change max change #iterations 9.797081 455.2827 at 10iterations 5.457249 145.5678 at 20iterations 3.028441 63.84996 at 30iterations 1.680142 32.20751 at 40iterations 0.9280319 18.01268 at 50iterations 0.5121683 10.17652 at 60iterations 0.2828852 6.634994 at 70iterations 0.1556418 2.862408 at 80iterations 8.5539207E-02 1.730294 at 90iterations 4.7085099E-02 0.8286095 at 100iterations 2.5862535E-02 0.4837494 at 110iterations 1.4235091E-02 0.2788191 at 120iterations 7.8271199E-03 0.1449413 at 130iterations 4.3027699E-03 8.0560684E-02 at 140iterations 2.3694658E-03 4.8152924E-02 at 150iterations 1.3014966E-03 2.2521973E-02 at 160iterations 7.1639166E-04 1.5063286E-02 at 170iterations 3.9458086E-04 7.2708130E-03 at 180iterations finished qdiffx linear iterations at : 11:40:03 total time elapsed so far: 19.80000 # loops : 180 mean,max change (kT/e) : 3.9458086E-04 7.2708130E-03 energy calculations done at 19.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.97000 DelPhi exited at 11:40:03 19.979u 0.505s 0:20.90 97.9% 0+0k 0+0io 0pf+0w