Sat Oct 8 18:16:40 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 Sat Oct 8 2011 at 18:16:40 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 = 3752 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: 0.5431300 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): -1.687000 60.34600 ymin,ymax (A): -18.58500 44.38600 zmin,zma (A): -6.439000 59.10700 x,y,z range (A): 62.03300 62.97100 65.54601 scale (grids/A): 0.5431300 object centre (A): 29.32950 12.90050 26.33400 number of atom coordinates read : 3752 total number of charged atoms : 3601 net assigned charge : -9.999962 assigned positive charge : 565.4844 centred at (gu) : 88.81232 86.79086 90.74865 assigned negative charge : -575.4868 centred at (gu) : 88.89326 86.80874 90.77962 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7205 nv = 96 ne = 84 npr = 75523 no. pairs analyzed = 75523 no. exposed pairs = 4880 no. arc points = 34579 no. surface atoms = 1625 nbur = 2127 mkacc time = 0.2100000 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 = 1.596000 m= 308 mr = 3676 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 3827 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3467 ## 434 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 9463 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7248565E-10 -9.5603359E-10 midg,1,midg; midg,igrid,midg -9.2052199E-10 -3.2269054E-10 1,midg,midg; igrid,midg,midg 7.8690811E-11 -8.8190244E-10 gauss-seidel spectral radius is 0.9825856 estimated iterations to convergence 62 setup time was (sec) 0.7300000 now iterating at: 18:16:41 rms-change max change #iterations 7.9040900E-02 14.05780 at 10iterations 5.4564415E-03 0.8656521 at 20iterations 5.6274183E-04 8.5559845E-02 at 30iterations 1.3372139E-04 2.0648003E-02 at 40iterations 4.0063049E-05 5.9852600E-03 at 50iterations finished qdiffx linear iterations at : 18:16:44 total time elapsed so far: 4.070000 # loops : 50 mean,max change (kT/e) : 4.0063049E-05 5.9852600E-03 energy calculations done at 4.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.250000 DelPhi exited at 18:16:45 4.252u 0.276s 0:04.86 93.0% 0+0k 0+0io 6pf+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 18:16:45 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 = 3752 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: 1.629390 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): -1.687000 60.34600 ymin,ymax (A): -18.58500 44.38600 zmin,zma (A): -6.439000 59.10700 x,y,z range (A): 62.03300 62.97100 65.54601 scale (grids/A): 1.629390 object centre (A): 29.32950 12.90050 26.33400 number of atom coordinates read : 3752 total number of charged atoms : 3601 net assigned charge : -9.999962 assigned positive charge : 565.4844 centred at (gu) : 86.43578 80.37148 92.24459 assigned negative charge : -575.4868 centred at (gu) : 86.67924 80.42594 92.33862 start vw surface at 0.1900000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 79510 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34579 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 24602 mr = 53516 m= 2491 mr = 16491 m= 60 mr = 1085 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 53 time to turn everything in is 0.7300000 number of dielectric boundary points 35571 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 413 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 27537 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) : 0.5431300 object centre at (A) : 29.32950 12.90050 26.33400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4015184E-04 -1.1383637E-02 midg,1,midg; midg,igrid,midg -2.6525047E-02 -7.1106949E-03 1,midg,midg; igrid,midg,midg -1.0261292E-02 -2.9539727E-02 gauss-seidel spectral radius is 0.9982505 estimated iterations to convergence 190 setup time was (sec) 1.030000 now iterating at: 18:16:46 rms-change max change #iterations 3.792336 183.8584 at 10iterations 1.601128 56.97751 at 20iterations 0.6767512 25.46465 at 30iterations 0.2860946 10.32149 at 40iterations 0.1213850 4.211992 at 50iterations 5.1464718E-02 2.007477 at 60iterations 2.1920273E-02 0.7335842 at 70iterations 9.3040802E-03 0.2829361 at 80iterations 3.9623538E-03 0.1236595 at 90iterations 1.7014823E-03 5.9794016E-02 at 100iterations 7.4290577E-04 2.9058456E-02 at 110iterations 3.3267951E-04 1.1370122E-02 at 120iterations finished qdiffx linear iterations at : 18:16:55 total time elapsed so far: 9.510000 # loops : 120 mean,max change (kT/e) : 3.3267951E-04 1.1370122E-02 energy calculations done at 9.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.700000 DelPhi exited at 18:16:55 9.698u 0.310s 0:10.29 97.1% 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 18:16:55 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 = 3752 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: 2.444085 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): -1.687000 60.34600 ymin,ymax (A): -18.58500 44.38600 zmin,zma (A): -6.439000 59.10700 x,y,z range (A): 62.03300 62.97100 65.54601 scale (grids/A): 2.444085 object centre (A): 29.32950 12.90050 26.33400 number of atom coordinates read : 3752 total number of charged atoms : 3601 net assigned charge : -9.999962 assigned positive charge : 565.4844 centred at (gu) : 84.65327 75.55708 93.36666 assigned negative charge : -575.4868 centred at (gu) : 85.01881 75.63872 93.50797 start vw surface at 0.1900000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 184827 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34579 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 85114 mr = 131382 m= 23993 mr = 66425 m= 3881 mr = 17590 m= 216 mr = 2312 m= 7 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 160 time to turn everything in is 1.760000 number of dielectric boundary points 80266 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 32 iepsmp to db, and charging done at 1.920000 number of grid points assigned charge 28758 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) : 1.629390 object centre at (A) : 29.32950 12.90050 26.33400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2853335E-02 3.6505412E-02 midg,1,midg; midg,igrid,midg -0.4057492 -9.5353842E-02 1,midg,midg; igrid,midg,midg -0.1693518 -0.5515935 gauss-seidel spectral radius is 0.9991742 estimated iterations to convergence 275 setup time was (sec) 2.100000 now iterating at: 18:16:58 rms-change max change #iterations 9.866344 271.5712 at 10iterations 5.615644 124.1108 at 20iterations 3.185801 68.04962 at 30iterations 1.794063 38.46613 at 40iterations 1.009120 21.35944 at 50iterations 0.5653204 10.31256 at 60iterations 0.3166969 6.810195 at 70iterations 0.1774954 3.472975 at 80iterations 9.9066742E-02 1.854653 at 90iterations 5.5225857E-02 1.000933 at 100iterations 3.0839099E-02 0.5931931 at 110iterations 1.7200930E-02 0.3138704 at 120iterations 9.5976368E-03 0.2019374 at 130iterations 5.3619011E-03 9.8391205E-02 at 140iterations 3.0000510E-03 5.9019089E-02 at 150iterations 1.6831090E-03 3.0363083E-02 at 160iterations 9.4481814E-04 1.9620895E-02 at 170iterations 5.3776283E-04 1.0330200E-02 at 180iterations finished qdiffx linear iterations at : 18:17:12 total time elapsed so far: 16.24000 # loops : 180 mean,max change (kT/e) : 5.3776283E-04 1.0330200E-02 energy calculations done at 16.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.43000 DelPhi exited at 18:17:12 16.432u 0.323s 0:17.03 98.3% 0+0k 0+0io 0pf+0w