Mon Oct 10 14:41:47 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 14:41:47 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5001 !!! WARNING: ASP 610 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= 0.1600000 grid size : 179 scale,in grids/A, set to be: 0.5209782 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): 7.447999 62.56400 ymin,ymax (A): -28.92400 39.40900 zmin,zma (A): -29.03800 33.57500 x,y,z range (A): 55.11600 68.33300 62.61300 scale (grids/A): 0.5209782 object centre (A): 35.00600 5.242500 2.268500 number of atom coordinates read : 5001 total number of charged atoms : 4841 net assigned charge : 1.000011 assigned positive charge : 748.9612 centred at (gu) : 89.68175 89.37292 89.11390 assigned negative charge : -747.9660 centred at (gu) : 89.64631 89.37104 89.12659 start vw surface at 0.2400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 8560 nv = 96 ne = 84 npr = 102699 no. pairs analyzed = 102699 no. exposed pairs = 6128 no. arc points = 40858 no. surface atoms = 2067 nbur = 2934 mkacc time = 0.3400000 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= 331 mr = 4654 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6800000 number of dielectric boundary points 4229 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4097 ## 548 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 11559 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.5050252E-11 -2.4395423E-11 midg,1,midg; midg,igrid,midg 1.6808636E-11 2.5779417E-11 1,midg,midg; igrid,midg,midg -1.3819679E-10 1.5668744E-10 gauss-seidel spectral radius is 0.9811658 estimated iterations to convergence 60 setup time was (sec) 1.020000 now iterating at: 14:41:48 rms-change max change #iterations 7.7674814E-02 12.81042 at 10iterations 5.0019007E-03 0.8657303 at 20iterations 7.9095270E-04 0.1276627 at 30iterations 2.9345509E-04 3.8623810E-02 at 40iterations 1.2477007E-04 1.5878677E-02 at 50iterations finished qdiffx linear iterations at : 14:41:52 total time elapsed so far: 4.900000 # loops : 50 mean,max change (kT/e) : 1.2477007E-04 1.5878677E-02 energy calculations done at 4.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.120000 DelPhi exited at 14:41:53 5.124u 0.437s 0:06.10 90.9% 0+0k 0+0io 5pf+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 14:41:53 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5001 !!! WARNING: ASP 610 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= 0.1600000 grid size : 179 scale,in grids/A, set to be: 1.562934 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): 7.447999 62.56400 ymin,ymax (A): -28.92400 39.40900 zmin,zma (A): -29.03800 33.57500 x,y,z range (A): 55.11600 68.33300 62.61300 scale (grids/A): 1.562934 object centre (A): 35.00600 5.242500 2.268500 number of atom coordinates read : 5001 total number of charged atoms : 4841 net assigned charge : 1.000011 assigned positive charge : 748.9612 centred at (gu) : 89.04360 88.11706 87.34017 assigned negative charge : -747.9660 centred at (gu) : 88.93848 88.11295 87.37940 start vw surface at 0.2300000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 97133 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40858 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 30246 mr = 68608 m= 2898 mr = 20822 m= 60 mr = 1422 m= 0 mr = 2 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 978 time to turn everything in is 1.010000 number of dielectric boundary points 39483 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 503 ## 4 charges are in solution ## iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 36613 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) : 0.5209782 object centre at (A) : 35.00600 5.242500 2.268500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4555863E-04 -1.3718809E-02 midg,1,midg; midg,igrid,midg 1.7930586E-02 -4.3110624E-03 1,midg,midg; igrid,midg,midg 1.6584650E-04 4.6167141E-03 gauss-seidel spectral radius is 0.9982117 estimated iterations to convergence 188 setup time was (sec) 1.380000 now iterating at: 14:41:55 rms-change max change #iterations 4.081256 161.3467 at 10iterations 1.707016 54.50695 at 20iterations 0.7187067 21.97016 at 30iterations 0.3007525 9.196772 at 40iterations 0.1268167 3.747772 at 50iterations 5.3487062E-02 1.796463 at 60iterations 2.2498494E-02 0.7064857 at 70iterations 9.5660416E-03 0.2801895 at 80iterations 4.1578659E-03 0.1347504 at 90iterations 1.8652696E-03 5.7106018E-02 at 100iterations 9.1798312E-04 2.8586388E-02 at 110iterations 5.2279927E-04 1.5853882E-02 at 120iterations finished qdiffx linear iterations at : 14:42:05 total time elapsed so far: 11.34000 # loops : 120 mean,max change (kT/e) : 5.2279927E-04 1.5853882E-02 energy calculations done at 11.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.56000 DelPhi exited at 14:42:06 11.566u 0.471s 0:12.42 96.8% 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 14:42:06 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5001 !!! WARNING: ASP 610 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= 0.1600000 grid size : 179 scale,in grids/A, set to be: 2.344402 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): 7.447999 62.56400 ymin,ymax (A): -28.92400 39.40900 zmin,zma (A): -29.03800 33.57500 x,y,z range (A): 55.11600 68.33300 62.61300 scale (grids/A): 2.344402 object centre (A): 35.00600 5.242500 2.268500 number of atom coordinates read : 5001 total number of charged atoms : 4841 net assigned charge : 1.000011 assigned positive charge : 748.9612 centred at (gu) : 88.56494 87.17527 86.00970 assigned negative charge : -747.9660 centred at (gu) : 88.40756 87.16934 86.06897 start vw surface at 0.2200000 fill in re-entrant regions at 0.7700000 boundary points on vw surface= 226579 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40858 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 105424 mr = 168443 m= 29160 mr = 83536 m= 4353 mr = 21852 m= 231 mr = 2786 m= 4 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 1.540000 no. cavity mid-points inaccessible to solvent = 3445 time to turn everything in is 2.470000 number of dielectric boundary points 89038 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 45 iepsmp to db, and charging done at 2.710000 number of grid points assigned charge 38643 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) : 1.562934 object centre at (A) : 35.00600 5.242500 2.268500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5922727E-02 -0.3403012 midg,1,midg; midg,igrid,midg 0.4773612 -0.1630594 1,midg,midg; igrid,midg,midg 5.6216933E-02 0.1182175 gauss-seidel spectral radius is 0.9991959 estimated iterations to convergence 278 setup time was (sec) 2.940000 now iterating at: 14:42:09 rms-change max change #iterations 10.92059 270.7867 at 10iterations 6.355707 170.3005 at 20iterations 3.678670 71.75235 at 30iterations 2.114283 60.61089 at 40iterations 1.209905 23.67847 at 50iterations 0.6883130 13.52415 at 60iterations 0.3915707 6.895758 at 70iterations 0.2221098 4.096174 at 80iterations 0.1256122 2.412615 at 90iterations 7.1209125E-02 1.191177 at 100iterations 4.0190529E-02 0.6765900 at 110iterations 2.2689771E-02 0.4147472 at 120iterations 1.2861559E-02 0.2405796 at 130iterations 7.3134797E-03 0.1274352 at 140iterations 4.1795745E-03 8.5787773E-02 at 150iterations 2.4293566E-03 4.1126251E-02 at 160iterations 1.4562511E-03 2.5257111E-02 at 170iterations 9.1303664E-04 1.7246246E-02 at 180iterations finished qdiffx linear iterations at : 14:42:26 total time elapsed so far: 20.04000 # loops : 180 mean,max change (kT/e) : 9.1303664E-04 1.7246246E-02 energy calculations done at 20.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.26000 DelPhi exited at 14:42:27 20.263u 0.537s 0:21.67 95.9% 0+0k 0+0io 0pf+0w