Sat Oct 8 17:15:39 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+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 Sat Oct 8 2011 at 17:15:39 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3399 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: 0.5634695 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): 35.94400 94.95600 ymin,ymax (A): 16.03600 79.21600 zmin,zma (A): -24.72900 27.56100 x,y,z range (A): 59.01200 63.18000 52.29000 scale (grids/A): 0.5634695 object centre (A): 65.45000 47.62600 1.415999 number of atom coordinates read : 3399 total number of charged atoms : 3253 net assigned charge : -5.999987 assigned positive charge : 514.0024 centred at (gu) : 89.68343 90.09654 89.72631 assigned negative charge : -520.0037 centred at (gu) : 89.69214 90.06449 89.70626 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7038 nv = 96 ne = 84 npr = 69205 no. pairs analyzed = 69205 no. exposed pairs = 4128 no. arc points = 28200 no. surface atoms = 1401 nbur = 1998 mkacc time = 0.2000000 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 = 1.540000 m= 285 mr = 3866 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 3446 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2968 ## 343 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 9102 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0892112E-09 -4.0702205E-10 midg,1,midg; midg,igrid,midg -1.1707961E-09 -2.6332439E-10 1,midg,midg; igrid,midg,midg -6.4391459E-10 -7.9295870E-10 gauss-seidel spectral radius is 0.9837799 estimated iterations to convergence 65 setup time was (sec) 0.7000000 now iterating at: 17:15:40 rms-change max change #iterations 9.3851224E-02 15.03167 at 10iterations 6.9019622E-03 1.005957 at 20iterations 5.6373107E-04 8.0131531E-02 at 30iterations 7.4336531E-05 1.3395309E-02 at 40iterations 1.6841430E-05 3.4456253E-03 at 50iterations finished qdiffx linear iterations at : 17:15:44 total time elapsed so far: 4.100000 # loops : 50 mean,max change (kT/e) : 1.6841430E-05 3.4456253E-03 energy calculations done at 4.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.290000 DelPhi exited at 17:15:44 4.290u 0.285s 0:04.84 94.4% 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 Sat Oct 8 2011 at 17:15:44 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3399 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: 1.690408 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): 35.94400 94.95600 ymin,ymax (A): 16.03600 79.21600 zmin,zma (A): -24.72900 27.56100 x,y,z range (A): 59.01200 63.18000 52.29000 scale (grids/A): 1.690408 object centre (A): 65.45000 47.62600 1.415999 number of atom coordinates read : 3399 total number of charged atoms : 3253 net assigned charge : -5.999987 assigned positive charge : 514.0024 centred at (gu) : 89.04928 90.28870 89.17813 assigned negative charge : -520.0037 centred at (gu) : 89.07616 90.19298 89.11847 start vw surface at 0.1900000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 77801 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28200 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 25829 mr = 54619 m= 2863 mr = 18402 m= 89 mr = 1506 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 108 time to turn everything in is 0.7100000 number of dielectric boundary points 32046 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 303 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 25115 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) : 0.5634695 object centre at (A) : 65.45000 47.62600 1.415999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.7862384E-03 -7.9943994E-03 midg,1,midg; midg,igrid,midg 3.0864028E-03 1.4493473E-02 1,midg,midg; igrid,midg,midg -2.0491976E-02 -7.8931525E-03 gauss-seidel spectral radius is 0.9983450 estimated iterations to convergence 195 setup time was (sec) 1.030000 now iterating at: 17:15:45 rms-change max change #iterations 3.900237 157.0468 at 10iterations 1.691046 53.75536 at 20iterations 0.7321429 21.98886 at 30iterations 0.3181860 10.31458 at 40iterations 0.1383635 4.527817 at 50iterations 6.0122300E-02 1.929280 at 60iterations 2.6211523E-02 0.8751965 at 70iterations 1.1386758E-02 0.3469410 at 80iterations 4.9632769E-03 0.1533732 at 90iterations 2.1674861E-03 6.9347024E-02 at 100iterations 9.5304823E-04 2.8262496E-02 at 110iterations 4.2656041E-04 1.4135361E-02 at 120iterations finished qdiffx linear iterations at : 17:15:54 total time elapsed so far: 9.650000 # loops : 120 mean,max change (kT/e) : 4.2656041E-04 1.4135361E-02 energy calculations done at 9.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.830000 DelPhi exited at 17:15:55 9.833u 0.325s 0:10.59 95.8% 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 8 2011 at 17:15:55 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3399 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: 2.535613 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): 35.94400 94.95600 ymin,ymax (A): 16.03600 79.21600 zmin,zma (A): -24.72900 27.56100 x,y,z range (A): 59.01200 63.18000 52.29000 scale (grids/A): 2.535613 object centre (A): 65.45000 47.62600 1.415999 number of atom coordinates read : 3399 total number of charged atoms : 3253 net assigned charge : -5.999987 assigned positive charge : 514.0024 centred at (gu) : 88.57391 90.43288 88.76704 assigned negative charge : -520.0037 centred at (gu) : 88.61401 90.28928 88.67767 start vw surface at 0.1800000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 180347 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28200 grid for indexing accessible points = 1.400000 m= 88044 mr = 132705 m= 26426 mr = 71187 m= 4679 mr = 20459 m= 391 mr = 3155 m= 8 mr = 197 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 435 time to turn everything in is 1.730000 number of dielectric boundary points 72192 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 26013 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) : 1.690408 object centre at (A) : 65.45000 47.62600 1.415999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2303430E-02 -8.5557282E-02 midg,1,midg; midg,igrid,midg 0.3114599 0.3353311 1,midg,midg; igrid,midg,midg -0.2617021 -7.6016478E-02 gauss-seidel spectral radius is 0.9991930 estimated iterations to convergence 278 setup time was (sec) 2.060000 now iterating at: 17:15:57 rms-change max change #iterations 9.851209 361.9366 at 10iterations 5.634618 146.4847 at 20iterations 3.202538 74.33521 at 30iterations 1.814194 33.87855 at 40iterations 1.022734 22.15972 at 50iterations 0.5794077 12.76093 at 60iterations 0.3255409 6.939032 at 70iterations 0.1826741 3.660046 at 80iterations 0.1026205 2.065619 at 90iterations 5.7710640E-02 1.047915 at 100iterations 3.2388613E-02 0.6042480 at 110iterations 1.8177202E-02 0.3392792 at 120iterations 1.0215961E-02 0.1880789 at 130iterations 5.7232552E-03 0.1105175 at 140iterations 3.2180410E-03 6.8170547E-02 at 150iterations 1.8061212E-03 3.3307552E-02 at 160iterations 1.0206444E-03 2.3459554E-02 at 170iterations 5.7821249E-04 1.0109425E-02 at 180iterations finished qdiffx linear iterations at : 17:16:12 total time elapsed so far: 16.44000 # loops : 180 mean,max change (kT/e) : 5.7821249E-04 1.0109425E-02 energy calculations done at 16.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.62000 DelPhi exited at 17:16:12 16.620u 0.349s 0:17.23 98.4% 0+0k 0+0io 0pf+0w