Sat Oct 8 14:42:09 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 14:42:09 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3033 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 0.5952679 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): -14.24100 35.98100 ymin,ymax (A): -14.40800 45.39700 zmin,zma (A): -40.84800 11.77500 x,y,z range (A): 50.22200 59.80500 52.62300 scale (grids/A): 0.5952679 object centre (A): 10.87000 15.49450 -14.53650 number of atom coordinates read : 3033 total number of charged atoms : 2886 net assigned charge : 1.4008060E-02 assigned positive charge : 455.4256 centred at (gu) : 91.37566 92.21215 91.10507 assigned negative charge : -455.4123 centred at (gu) : 91.41714 92.12496 91.16309 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6938 nv = 96 ne = 84 npr = 63874 no. pairs analyzed = 63874 no. exposed pairs = 3449 no. arc points = 23940 no. surface atoms = 1180 nbur = 1853 mkacc time = 0.1700000 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= 279 mr = 3969 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3226 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2396 ## 246 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8842 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6162879E-09 -2.7985498E-09 midg,1,midg; midg,igrid,midg -1.9513453E-09 5.2856981E-09 1,midg,midg; igrid,midg,midg 1.0837562E-09 -2.1379867E-09 gauss-seidel spectral radius is 0.9854217 estimated iterations to convergence 68 setup time was (sec) 0.6800000 now iterating at: 14:42:10 rms-change max change #iterations 0.1143543 20.21918 at 10iterations 9.8043075E-03 1.518959 at 20iterations 9.0535590E-04 0.1345940 at 30iterations 1.0221332E-04 1.3205484E-02 at 40iterations 1.6113672E-05 2.2742748E-03 at 50iterations finished qdiffx linear iterations at : 14:42:14 total time elapsed so far: 5.080000 # loops : 50 mean,max change (kT/e) : 1.6113672E-05 2.2742748E-03 energy calculations done at 5.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.240000 DelPhi exited at 14:42:15 5.243u 0.492s 0:05.99 95.6% 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 14:42:15 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3033 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 1.785804 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): -14.24100 35.98100 ymin,ymax (A): -14.40800 45.39700 zmin,zma (A): -40.84800 11.77500 x,y,z range (A): 50.22200 59.80500 52.62300 scale (grids/A): 1.785804 object centre (A): 10.87000 15.49450 -14.53650 number of atom coordinates read : 3033 total number of charged atoms : 2886 net assigned charge : 1.4008060E-02 assigned positive charge : 455.4256 centred at (gu) : 94.12621 96.63599 93.31493 assigned negative charge : -455.4123 centred at (gu) : 94.25113 96.37454 93.48890 start vw surface at 0.1200000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 76753 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23940 grid for indexing accessible points = 1.400000 m= 25270 mr = 55123 m= 2955 mr = 18592 m= 105 mr = 1588 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 29759 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 209 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 22491 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) : 0.5952679 object centre at (A) : 10.87000 15.49450 -14.53650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9644973E-03 6.4514116E-03 midg,1,midg; midg,igrid,midg -2.0096527E-02 3.8360886E-02 1,midg,midg; igrid,midg,midg 2.6984182E-03 -1.1024925E-02 gauss-seidel spectral radius is 0.9984808 estimated iterations to convergence 203 setup time was (sec) 0.9900000 now iterating at: 14:42:16 rms-change max change #iterations 4.074882 175.0482 at 10iterations 1.831208 66.14849 at 20iterations 0.8228146 25.89427 at 30iterations 0.3718327 11.88317 at 40iterations 0.1674944 5.106615 at 50iterations 7.5418577E-02 2.748639 at 60iterations 3.3881284E-02 1.105065 at 70iterations 1.5283855E-02 0.5019875 at 80iterations 6.8962318E-03 0.2181061 at 90iterations 3.1026369E-03 0.1098022 at 100iterations 1.4117646E-03 5.1347733E-02 at 110iterations 6.3236867E-04 2.0023346E-02 at 120iterations finished qdiffx linear iterations at : 14:42:28 total time elapsed so far: 12.21000 # loops : 120 mean,max change (kT/e) : 6.3236867E-04 2.0023346E-02 energy calculations done at 12.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.37000 DelPhi exited at 14:42:28 12.377u 0.549s 0:13.19 97.8% 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 14:42:28 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3033 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 2.678706 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): -14.24100 35.98100 ymin,ymax (A): -14.40800 45.39700 zmin,zma (A): -40.84800 11.77500 x,y,z range (A): 50.22200 59.80500 52.62300 scale (grids/A): 2.678706 object centre (A): 10.87000 15.49450 -14.53650 number of atom coordinates read : 3033 total number of charged atoms : 2886 net assigned charge : 1.4008060E-02 assigned positive charge : 455.4256 centred at (gu) : 96.18909 99.95400 94.97224 assigned negative charge : -455.4123 centred at (gu) : 96.37662 99.56169 95.23325 start vw surface at 0.1300000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 178388 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23940 grid for indexing accessible points = 1.400000 m= 86688 mr = 134080 m= 26622 mr = 71160 m= 4835 mr = 20872 m= 416 mr = 3428 m= 8 mr = 197 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.650000 number of dielectric boundary points 67220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 23082 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) : 1.785804 object centre at (A) : 10.87000 15.49450 -14.53650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.1220254E-02 0.2027937 midg,1,midg; midg,igrid,midg -0.1901141 0.5813509 1,midg,midg; igrid,midg,midg 5.9192970E-02 -8.9430355E-02 gauss-seidel spectral radius is 0.9992179 estimated iterations to convergence 282 setup time was (sec) 2.050000 now iterating at: 14:42:31 rms-change max change #iterations 9.844000 307.6791 at 10iterations 5.675393 132.1932 at 20iterations 3.248068 70.88951 at 30iterations 1.856851 34.68466 at 40iterations 1.059097 20.64820 at 50iterations 0.6014267 11.76105 at 60iterations 0.3415724 6.142842 at 70iterations 0.1947435 3.468622 at 80iterations 0.1104254 2.070641 at 90iterations 6.2676333E-02 1.160776 at 100iterations 3.5482824E-02 0.7112389 at 110iterations 2.0113911E-02 0.3958092 at 120iterations 1.1408717E-02 0.2073197 at 130iterations 6.4676325E-03 0.1168842 at 140iterations 3.6795728E-03 7.2467804E-02 at 150iterations 2.0871307E-03 3.9789200E-02 at 160iterations 1.1892887E-03 2.1774292E-02 at 170iterations 6.7959906E-04 1.2578011E-02 at 180iterations finished qdiffx linear iterations at : 14:42:50 total time elapsed so far: 20.86000 # loops : 180 mean,max change (kT/e) : 6.7959906E-04 1.2578011E-02 energy calculations done at 20.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.02000 DelPhi exited at 14:42:50 21.028u 0.552s 0:21.84 98.7% 0+0k 0+0io 0pf+0w