Sat Oct 15 14:28:21 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 15 2011 at 14:28:21 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 = 3007 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5255854 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): -11.06500 36.09000 ymin,ymax (A): -33.38700 34.34700 zmin,zma (A): 3.368000 51.84400 x,y,z range (A): 47.15500 67.73400 48.47600 scale (grids/A): 0.5255854 object centre (A): 12.51250 0.4799995 27.60600 number of atom coordinates read : 3007 total number of charged atoms : 2865 net assigned charge : -5.999968 assigned positive charge : 451.4069 centred at (gu) : 90.13297 90.58031 90.81337 assigned negative charge : -457.4081 centred at (gu) : 90.10947 90.62952 90.71128 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5324 nv = 96 ne = 84 npr = 60177 no. pairs analyzed = 60177 no. exposed pairs = 4035 no. arc points = 28619 no. surface atoms = 1349 nbur = 1658 mkacc time = 0.1100000 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= 203 mr = 2561 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 2959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2816 ## 378 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 7059 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9403131E-10 1.8379366E-10 midg,1,midg; midg,igrid,midg -1.2555060E-11 -3.6903350E-10 1,midg,midg; igrid,midg,midg -2.2995669E-10 -9.5329314E-11 gauss-seidel spectral radius is 0.9813587 estimated iterations to convergence 60 setup time was (sec) 0.5200000 now iterating at: 14:28:22 rms-change max change #iterations 5.9267078E-02 11.08553 at 10iterations 3.5861009E-03 0.6294403 at 20iterations 2.1096514E-04 3.7852287E-02 at 30iterations 1.2459241E-05 2.2459030E-03 at 40iterations 7.5112820E-07 1.2969971E-04 at 50iterations finished qdiffx linear iterations at : 14:28:25 total time elapsed so far: 3.670000 # loops : 50 mean,max change (kT/e) : 7.5112820E-07 1.2969971E-04 energy calculations done at 3.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.810000 DelPhi exited at 14:28:26 3.813u 0.294s 0:04.83 84.8% 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 Sat Oct 15 2011 at 14:28:26 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 = 3007 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.576756 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): -11.06500 36.09000 ymin,ymax (A): -33.38700 34.34700 zmin,zma (A): 3.368000 51.84400 x,y,z range (A): 47.15500 67.73400 48.47600 scale (grids/A): 1.576756 object centre (A): 12.51250 0.4799995 27.60600 number of atom coordinates read : 3007 total number of charged atoms : 2865 net assigned charge : -5.999968 assigned positive charge : 451.4069 centred at (gu) : 90.39788 91.74006 92.43918 assigned negative charge : -457.4081 centred at (gu) : 90.32808 91.88829 92.13359 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 59788 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28619 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 16852 mr = 39150 m= 1491 mr = 10815 m= 31 mr = 608 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 903 time to turn everything in is 0.3100000 number of dielectric boundary points 27589 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 375 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 21780 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) : 0.5255854 object centre at (A) : 12.51250 0.4799995 27.60600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3113035E-02 5.2832719E-03 midg,1,midg; midg,igrid,midg -1.2628599E-02 -9.7677307E-03 1,midg,midg; igrid,midg,midg -3.1710565E-03 -2.1439297E-03 gauss-seidel spectral radius is 0.9980530 estimated iterations to convergence 180 setup time was (sec) 0.5400000 now iterating at: 14:28:27 rms-change max change #iterations 3.075584 140.7816 at 10iterations 1.235310 54.35841 at 20iterations 0.4988883 21.17242 at 30iterations 0.2003689 8.239161 at 40iterations 8.0859527E-02 3.559440 at 50iterations 3.2712318E-02 1.241964 at 60iterations 1.3127620E-02 0.5258994 at 70iterations 5.3275460E-03 0.2305603 at 80iterations 2.1519260E-03 8.3993912E-02 at 90iterations 8.6791522E-04 3.2424927E-02 at 100iterations 3.5187829E-04 1.3255119E-02 at 110iterations 1.4208106E-04 5.6266785E-03 at 120iterations finished qdiffx linear iterations at : 14:28:35 total time elapsed so far: 8.160000 # loops : 120 mean,max change (kT/e) : 1.4208106E-04 5.6266785E-03 energy calculations done at 8.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.290000 DelPhi exited at 14:28:35 8.288u 0.252s 0:08.88 96.0% 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 15 2011 at 14:28:35 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 = 3007 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.365134 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): -11.06500 36.09000 ymin,ymax (A): -33.38700 34.34700 zmin,zma (A): 3.368000 51.84400 x,y,z range (A): 47.15500 67.73400 48.47600 scale (grids/A): 2.365134 object centre (A): 12.51250 0.4799995 27.60600 number of atom coordinates read : 3007 total number of charged atoms : 2865 net assigned charge : -5.999968 assigned positive charge : 451.4069 centred at (gu) : 90.59678 92.60995 93.65868 assigned negative charge : -457.4081 centred at (gu) : 90.49200 92.83231 93.20029 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 139012 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28619 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 59908 mr = 96589 m= 15362 mr = 45655 m= 2117 mr = 10732 m= 110 mr = 1245 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 3247 time to turn everything in is 0.7600000 number of dielectric boundary points 62267 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 29 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 22883 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) : 1.576756 object centre at (A) : 12.51250 0.4799995 27.60600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2100319 0.1278366 midg,1,midg; midg,igrid,midg -0.2652200 -0.1623915 1,midg,midg; igrid,midg,midg -4.8829481E-02 -3.6092754E-02 gauss-seidel spectral radius is 0.9990990 estimated iterations to convergence 263 setup time was (sec) 1.010000 now iterating at: 14:28:36 rms-change max change #iterations 8.210221 293.3854 at 10iterations 4.540192 122.2592 at 20iterations 2.493360 54.86241 at 30iterations 1.362912 31.47694 at 40iterations 0.7444610 16.40233 at 50iterations 0.4043919 9.387465 at 60iterations 0.2204286 4.926592 at 70iterations 0.1195222 2.705038 at 80iterations 6.4869471E-02 1.553750 at 90iterations 3.5174545E-02 0.7268081 at 100iterations 1.9077485E-02 0.4601479 at 110iterations 1.0279687E-02 0.2366333 at 120iterations 5.5804909E-03 0.1165581 at 130iterations 3.0263057E-03 6.6181183E-02 at 140iterations 1.6372948E-03 3.7122726E-02 at 150iterations 8.8561815E-04 1.9099236E-02 at 160iterations 4.7894614E-04 1.0520220E-02 at 170iterations 2.5917249E-04 5.6438446E-03 at 180iterations finished qdiffx linear iterations at : 14:28:49 total time elapsed so far: 12.79000 # loops : 180 mean,max change (kT/e) : 2.5917249E-04 5.6438446E-03 energy calculations done at 12.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.93000 DelPhi exited at 14:28:49 12.932u 0.287s 0:14.11 93.6% 0+0k 0+0io 0pf+0w