Sun Oct 9 01:56:15 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 01:56:15 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 = 2416 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6339596 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): 14.19300 68.12800 ymin,ymax (A): -30.55600 25.59900 zmin,zma (A): 2.565000 45.84700 x,y,z range (A): 53.93500 56.15500 43.28200 scale (grids/A): 0.6339596 object centre (A): 41.16050 -2.478499 24.20600 number of atom coordinates read : 2416 total number of charged atoms : 2281 net assigned charge : 11.50002 assigned positive charge : 353.1582 centred at (gu) : 89.81331 90.58765 89.48491 assigned negative charge : -341.6591 centred at (gu) : 89.82567 90.61153 89.59196 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6859 nv = 96 ne = 84 npr = 47269 no. pairs analyzed = 47269 no. exposed pairs = 3197 no. arc points = 22789 no. surface atoms = 1081 nbur = 1335 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 400 mr = 3642 m= 4 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3578 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2303 ## 242 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8039 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5914941E-08 4.1769970E-09 midg,1,midg; midg,igrid,midg 1.4224100E-08 1.3472786E-08 1,midg,midg; igrid,midg,midg 1.5687499E-08 1.2445250E-08 gauss-seidel spectral radius is 0.9871056 estimated iterations to convergence 72 setup time was (sec) 0.3700000 now iterating at: 01:56:15 rms-change max change #iterations 0.1325784 24.66356 at 10iterations 1.2730636E-02 1.977892 at 20iterations 1.3320851E-03 0.1808167 at 30iterations 2.2267485E-04 4.3624878E-02 at 40iterations 7.1985436E-05 1.5823364E-02 at 50iterations finished qdiffx linear iterations at : 01:56:18 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 7.1985436E-05 1.5823364E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 01:56:18 3.335u 0.166s 0:03.77 92.5% 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 Sun Oct 9 2011 at 01:56:18 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 = 2416 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.901879 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): 14.19300 68.12800 ymin,ymax (A): -30.55600 25.59900 zmin,zma (A): 2.565000 45.84700 x,y,z range (A): 53.93500 56.15500 43.28200 scale (grids/A): 1.901879 object centre (A): 41.16050 -2.478499 24.20600 number of atom coordinates read : 2416 total number of charged atoms : 2281 net assigned charge : 11.50002 assigned positive charge : 353.1582 centred at (gu) : 89.43947 91.76248 88.45441 assigned negative charge : -341.6591 centred at (gu) : 89.47697 91.83459 88.77593 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 73187 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22789 grid for indexing accessible points = 1.400000 m= 27020 mr = 49653 m= 4593 mr = 19601 m= 299 mr = 2851 m= 8 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 32907 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 183 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 17950 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) : 0.6339596 object centre at (A) : 41.16050 -2.478499 24.20600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9238133E-02 -1.3943447E-04 midg,1,midg; midg,igrid,midg 5.6764483E-02 2.4830263E-02 1,midg,midg; igrid,midg,midg 5.9580438E-02 4.6497788E-02 gauss-seidel spectral radius is 0.9986265 estimated iterations to convergence 214 setup time was (sec) 0.5800000 now iterating at: 01:56:19 rms-change max change #iterations 3.974598 198.5862 at 10iterations 1.844171 67.97778 at 20iterations 0.8624992 30.40086 at 30iterations 0.3995972 13.44968 at 40iterations 0.1867578 5.652260 at 50iterations 8.7239243E-02 3.043214 at 60iterations 4.0801089E-02 1.241029 at 70iterations 1.9032313E-02 0.6352997 at 80iterations 8.9109205E-03 0.3115921 at 90iterations 4.1772900E-03 0.1343575 at 100iterations 1.9745801E-03 6.9220543E-02 at 110iterations 9.4711938E-04 3.4983158E-02 at 120iterations finished qdiffx linear iterations at : 01:56:26 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 9.4711938E-04 3.4983158E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 01:56:27 7.691u 0.187s 0:08.16 96.4% 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 01:56:27 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 = 2416 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.852818 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): 14.19300 68.12800 ymin,ymax (A): -30.55600 25.59900 zmin,zma (A): 2.565000 45.84700 x,y,z range (A): 53.93500 56.15500 43.28200 scale (grids/A): 2.852818 object centre (A): 41.16050 -2.478499 24.20600 number of atom coordinates read : 2416 total number of charged atoms : 2281 net assigned charge : 11.50002 assigned positive charge : 353.1582 centred at (gu) : 89.15900 92.64365 87.68141 assigned negative charge : -341.6591 centred at (gu) : 89.21555 92.75195 88.16387 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 169308 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22789 grid for indexing accessible points = 1.400000 m= 85996 mr = 120910 m= 32007 mr = 69653 m= 8311 mr = 25441 m= 1284 mr = 6134 m= 84 mr = 798 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9300000 number of dielectric boundary points 74041 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 18246 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) : 1.901879 object centre at (A) : 41.16050 -2.478499 24.20600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2923511 -1.7175026E-02 midg,1,midg; midg,igrid,midg 0.7524075 0.3005450 1,midg,midg; igrid,midg,midg 0.6518902 0.4823644 gauss-seidel spectral radius is 0.9992613 estimated iterations to convergence 290 setup time was (sec) 1.160000 now iterating at: 01:56:28 rms-change max change #iterations 9.387871 466.0164 at 10iterations 5.489742 128.4636 at 20iterations 3.190201 72.38677 at 30iterations 1.855049 40.98050 at 40iterations 1.075239 25.84847 at 50iterations 0.6224811 11.79944 at 60iterations 0.3586231 7.848022 at 70iterations 0.2075487 4.158510 at 80iterations 0.1194411 2.283325 at 90iterations 6.8808571E-02 1.421333 at 100iterations 3.9686017E-02 0.7673950 at 110iterations 2.2827258E-02 0.4495659 at 120iterations 1.3154294E-02 0.2644672 at 130iterations 7.5500850E-03 0.1626816 at 140iterations 4.3536192E-03 7.7077866E-02 at 150iterations 2.5036160E-03 4.3797493E-02 at 160iterations 1.4465342E-03 2.7283192E-02 at 170iterations 8.3663821E-04 1.5766144E-02 at 180iterations finished qdiffx linear iterations at : 01:56:39 total time elapsed so far: 12.45000 # loops : 180 mean,max change (kT/e) : 8.3663821E-04 1.5766144E-02 energy calculations done at 12.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.58000 DelPhi exited at 01:56:40 12.586u 0.193s 0:13.08 97.6% 0+0k 0+0io 0pf+0w