Sun Oct 9 00:00:13 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 Sun Oct 9 2011 at 00:00:13 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2783 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5844977 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): 10.75300 71.33300 ymin,ymax (A): 99.91100 160.8180 zmin,zma (A): -0.3750000 45.81300 x,y,z range (A): 60.58000 60.90700 46.18800 scale (grids/A): 0.5844977 object centre (A): 41.04300 130.3645 22.71900 number of atom coordinates read : 2783 total number of charged atoms : 2643 net assigned charge : 7.240026 assigned positive charge : 409.1646 centred at (gu) : 89.15076 89.80369 90.11633 assigned negative charge : -401.9257 centred at (gu) : 89.30508 89.68594 90.11776 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6493 nv = 96 ne = 84 npr = 55719 no. pairs analyzed = 55719 no. exposed pairs = 3552 no. arc points = 25364 no. surface atoms = 1186 nbur = 1597 mkacc time = 0.1600000 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 = 1.456000 m= 272 mr = 3426 m= 0 mr = 16 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3323 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2499 ## 260 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8091 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8090089E-09 1.8385785E-09 midg,1,midg; midg,igrid,midg -9.8150721E-10 4.3044888E-09 1,midg,midg; igrid,midg,midg 6.4911871E-09 -1.4614485E-09 gauss-seidel spectral radius is 0.9848818 estimated iterations to convergence 67 setup time was (sec) 0.6400000 now iterating at: 00:00:14 rms-change max change #iterations 9.9072464E-02 16.83194 at 10iterations 7.7884723E-03 1.244961 at 20iterations 6.2538835E-04 0.1121597 at 30iterations 4.9949158E-05 8.4013939E-03 at 40iterations 4.0783129E-06 6.7329407E-04 at 50iterations finished qdiffx linear iterations at : 00:00:17 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 4.0783129E-06 6.7329407E-04 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.090000 DelPhi exited at 00:00:18 4.089u 0.240s 0:04.60 93.9% 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 00:00:18 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2783 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.753493 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): 10.75300 71.33300 ymin,ymax (A): 99.91100 160.8180 zmin,zma (A): -0.3750000 45.81300 x,y,z range (A): 60.58000 60.90700 46.18800 scale (grids/A): 1.753493 object centre (A): 41.04300 130.3645 22.71900 number of atom coordinates read : 2783 total number of charged atoms : 2643 net assigned charge : 7.240026 assigned positive charge : 409.1646 centred at (gu) : 87.45168 89.41057 90.34839 assigned negative charge : -401.9257 centred at (gu) : 87.91513 89.05765 90.35304 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 71222 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25364 grid for indexing accessible points = 1.400000 m= 24209 mr = 48657 m= 2961 mr = 17386 m= 113 mr = 1632 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 415 time to turn everything in is 0.6300000 number of dielectric boundary points 30807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 211 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 20537 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) : 0.5844977 object centre at (A) : 41.04300 130.3645 22.71900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5368934E-02 1.2981378E-02 midg,1,midg; midg,igrid,midg -1.4930818E-02 2.6251127E-03 1,midg,midg; igrid,midg,midg 4.3128412E-02 -3.0629214E-02 gauss-seidel spectral radius is 0.9984207 estimated iterations to convergence 200 setup time was (sec) 0.9300000 now iterating at: 00:00:19 rms-change max change #iterations 3.726769 161.1129 at 10iterations 1.638297 82.44755 at 20iterations 0.7224268 24.23565 at 30iterations 0.3187907 10.24579 at 40iterations 0.1409743 4.589067 at 50iterations 6.2281482E-02 2.062117 at 60iterations 2.7526097E-02 0.9193821 at 70iterations 1.2150375E-02 0.4634001 at 80iterations 5.3854864E-03 0.1858788 at 90iterations 2.3805858E-03 7.8207016E-02 at 100iterations 1.0521956E-03 3.4694672E-02 at 110iterations 4.6620553E-04 1.5227914E-02 at 120iterations finished qdiffx linear iterations at : 00:00:27 total time elapsed so far: 9.120000 # loops : 120 mean,max change (kT/e) : 4.6620553E-04 1.5227914E-02 energy calculations done at 9.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.300000 DelPhi exited at 00:00:28 9.299u 0.302s 0:09.87 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 Sun Oct 9 2011 at 00:00:28 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2783 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.630240 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): 10.75300 71.33300 ymin,ymax (A): 99.91100 160.8180 zmin,zma (A): -0.3750000 45.81300 x,y,z range (A): 60.58000 60.90700 46.18800 scale (grids/A): 2.630240 object centre (A): 41.04300 130.3645 22.71900 number of atom coordinates read : 2783 total number of charged atoms : 2643 net assigned charge : 7.240026 assigned positive charge : 409.1646 centred at (gu) : 86.17741 89.11561 90.52253 assigned negative charge : -401.9257 centred at (gu) : 86.87273 88.58634 90.52959 start vw surface at 0.1700000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 164685 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25364 grid for indexing accessible points = 1.400000 m= 80609 mr = 118340 m= 26366 mr = 65012 m= 5143 mr = 20616 m= 478 mr = 3602 m= 7 mr = 248 m= 0 mr = 2 time to grow re-entrant surface = 0.9399999 no. cavity mid-points inaccessible to solvent = 1320 time to turn everything in is 1.580000 number of dielectric boundary points 69468 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 21122 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) : 1.753493 object centre at (A) : 41.04300 130.3645 22.71900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1900575 0.1334949 midg,1,midg; midg,igrid,midg -0.2098391 -3.6619473E-03 1,midg,midg; igrid,midg,midg 0.7408131 -0.5823702 gauss-seidel spectral radius is 0.9992052 estimated iterations to convergence 280 setup time was (sec) 1.890000 now iterating at: 00:00:30 rms-change max change #iterations 9.163780 307.4716 at 10iterations 5.249538 120.4047 at 20iterations 2.979727 65.50851 at 30iterations 1.681652 36.63875 at 40iterations 0.9488520 19.77938 at 50iterations 0.5363097 11.25613 at 60iterations 0.3012439 5.640645 at 70iterations 0.1693260 3.437346 at 80iterations 9.5291674E-02 1.840576 at 90iterations 5.3594369E-02 1.023560 at 100iterations 3.0050460E-02 0.5857124 at 110iterations 1.6922643E-02 0.3189430 at 120iterations 9.5252274E-03 0.1685638 at 130iterations 5.3519118E-03 0.1117706 at 140iterations 3.0089892E-03 5.9604645E-02 at 150iterations 1.6915686E-03 3.2225132E-02 at 160iterations 9.4878674E-04 1.8479347E-02 at 170iterations 5.3449266E-04 9.9925995E-03 at 180iterations finished qdiffx linear iterations at : 00:00:43 total time elapsed so far: 15.32000 # loops : 180 mean,max change (kT/e) : 5.3449266E-04 9.9925995E-03 energy calculations done at 15.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.50000 DelPhi exited at 00:00:44 15.501u 0.310s 0:16.07 98.3% 0+0k 0+0io 0pf+0w