Sun Oct 9 01:47:39 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 Sun Oct 9 2011 at 01:47:39 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3341 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 0.5849779 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): -40.85400 16.39000 ymin,ymax (A): -11.99200 48.72900 zmin,zma (A): -51.49300 9.364000 x,y,z range (A): 57.24400 60.72100 60.85700 scale (grids/A): 0.5849779 object centre (A): -12.23200 18.36850 -21.06450 number of atom coordinates read : 3341 total number of charged atoms : 3198 net assigned charge : 11.22604 assigned positive charge : 495.8526 centred at (gu) : 89.69270 90.44436 92.48521 assigned negative charge : -484.6283 centred at (gu) : 89.80254 90.38283 92.72982 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7847 nv = 96 ne = 84 npr = 64981 no. pairs analyzed = 64981 no. exposed pairs = 4458 no. arc points = 32083 no. surface atoms = 1479 nbur = 1862 mkacc time = 0.1400000 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= 351 mr = 4000 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3300000 number of dielectric boundary points 4168 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3335 ## 396 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9909 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5037805E-09 -7.3973694E-09 midg,1,midg; midg,igrid,midg 1.2191111E-09 5.3009055E-09 1,midg,midg; igrid,midg,midg 6.5621268E-09 -2.9390452E-11 gauss-seidel spectral radius is 0.9849588 estimated iterations to convergence 67 setup time was (sec) 0.5600000 now iterating at: 01:47:40 rms-change max change #iterations 0.1063273 21.84874 at 10iterations 8.4774718E-03 1.174402 at 20iterations 7.0933346E-04 0.1073761 at 30iterations 6.5547043E-05 8.7776184E-03 at 40iterations 8.4102885E-06 9.3078613E-04 at 50iterations finished qdiffx linear iterations at : 01:47:42 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 8.4102885E-06 9.3078613E-04 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 01:47:43 3.159u 0.139s 0:03.84 85.4% 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 Sun Oct 9 2011 at 01:47:43 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3341 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 1.754934 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): -40.85400 16.39000 ymin,ymax (A): -11.99200 48.72900 zmin,zma (A): -51.49300 9.364000 x,y,z range (A): 57.24400 60.72100 60.85700 scale (grids/A): 1.754934 object centre (A): -12.23200 18.36850 -21.06450 number of atom coordinates read : 3341 total number of charged atoms : 3198 net assigned charge : 11.22604 assigned positive charge : 495.8526 centred at (gu) : 89.07736 91.33216 97.45458 assigned negative charge : -484.6283 centred at (gu) : 89.40717 91.14816 98.18932 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 86025 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32083 grid for indexing accessible points = 1.400000 m= 27941 mr = 57784 m= 3456 mr = 19331 m= 124 mr = 1843 m= 0 mr = 12 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 975 time to turn everything in is 0.6200000 number of dielectric boundary points 38576 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 304 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 24906 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) : 0.5849779 object centre at (A) : -12.23200 18.36850 -21.06450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0113304E-02 -2.7421021E-03 midg,1,midg; midg,igrid,midg 3.1134350E-02 5.3725772E-02 1,midg,midg; igrid,midg,midg 1.4429435E-02 -7.0415377E-03 gauss-seidel spectral radius is 0.9984852 estimated iterations to convergence 204 setup time was (sec) 1.020000 now iterating at: 01:47:44 rms-change max change #iterations 4.158316 178.9120 at 10iterations 1.850039 63.64029 at 20iterations 0.8276904 27.83611 at 30iterations 0.3712520 12.68076 at 40iterations 0.1671754 5.299028 at 50iterations 7.5065687E-02 2.525356 at 60iterations 3.3591226E-02 1.045883 at 70iterations 1.5110117E-02 0.4597282 at 80iterations 6.7917323E-03 0.2163525 at 90iterations 3.0485084E-03 0.1117172 at 100iterations 1.3747656E-03 4.3800831E-02 at 110iterations 6.1809685E-04 2.2310257E-02 at 120iterations finished qdiffx linear iterations at : 01:47:53 total time elapsed so far: 10.10000 # loops : 120 mean,max change (kT/e) : 6.1809685E-04 2.2310257E-02 energy calculations done at 10.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.28000 DelPhi exited at 01:47:54 10.280u 0.349s 0:10.96 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 Sun Oct 9 2011 at 01:47:54 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3341 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 2.632401 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): -40.85400 16.39000 ymin,ymax (A): -11.99200 48.72900 zmin,zma (A): -51.49300 9.364000 x,y,z range (A): 57.24400 60.72100 60.85700 scale (grids/A): 2.632401 object centre (A): -12.23200 18.36850 -21.06450 number of atom coordinates read : 3341 total number of charged atoms : 3198 net assigned charge : 11.22604 assigned positive charge : 495.8526 centred at (gu) : 88.61581 91.99800 101.1819 assigned negative charge : -484.6283 centred at (gu) : 89.11077 91.72223 102.2839 start vw surface at 0.1600000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 199233 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32083 grid for indexing accessible points = 1.400000 m= 94059 mr = 141033 m= 29757 mr = 74296 m= 5789 mr = 22714 m= 550 mr = 3923 m= 15 mr = 270 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 3071 time to turn everything in is 1.470000 number of dielectric boundary points 87166 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 25559 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) : 1.754934 object centre at (A) : -12.23200 18.36850 -21.06450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3920475 -6.8676069E-02 midg,1,midg; midg,igrid,midg 0.5834980 0.7763870 1,midg,midg; igrid,midg,midg 0.1407564 -1.9820133E-02 gauss-seidel spectral radius is 0.9992494 estimated iterations to convergence 288 setup time was (sec) 1.770000 now iterating at: 01:47:56 rms-change max change #iterations 10.28786 270.9131 at 10iterations 6.048501 147.7887 at 20iterations 3.526322 81.96906 at 30iterations 2.052889 51.69421 at 40iterations 1.184893 23.98928 at 50iterations 0.6841031 13.37557 at 60iterations 0.3943096 7.815408 at 70iterations 0.2266572 4.339570 at 80iterations 0.1302206 2.239712 at 90iterations 7.4683473E-02 1.575699 at 100iterations 4.2881634E-02 0.8279390 at 110iterations 2.4535144E-02 0.4167575 at 120iterations 1.4041408E-02 0.2481041 at 130iterations 8.0668107E-03 0.1364374 at 140iterations 4.6154633E-03 8.6217880E-02 at 150iterations 2.6387705E-03 4.6066284E-02 at 160iterations 1.5097010E-03 2.5035858E-02 at 170iterations 8.6442183E-04 1.5211105E-02 at 180iterations finished qdiffx linear iterations at : 01:48:07 total time elapsed so far: 12.69000 # loops : 180 mean,max change (kT/e) : 8.6442183E-04 1.5211105E-02 energy calculations done at 12.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.87000 DelPhi exited at 01:48:07 12.872u 0.208s 0:13.37 97.7% 0+0k 0+0io 0pf+0w