Tue Oct 11 05:49:25 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 Tue Oct 11 2011 at 05:49:26 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 = 2034 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7080632 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): -20.18000 23.80600 ymin,ymax (A): -11.97000 28.73700 zmin,zma (A): -3.482000 46.79600 x,y,z range (A): 43.98600 40.70700 50.27800 scale (grids/A): 0.7080632 object centre (A): 1.813000 8.383500 21.65700 number of atom coordinates read : 2034 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 90.16953 89.67368 90.47549 assigned negative charge : -304.2972 centred at (gu) : 89.99100 89.69512 90.50256 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6939 nv = 96 ne = 84 npr = 40493 no. pairs analyzed = 40493 no. exposed pairs = 2443 no. arc points = 16681 no. surface atoms = 838 nbur = 1196 mkacc time = 5.9999995E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 454 mr = 4000 m= 4 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 7.0000000E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3327 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1635 ## 151 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7774 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.0721370E-08 5.5573999E-08 midg,1,midg; midg,igrid,midg 7.9406909E-08 5.0514124E-08 1,midg,midg; igrid,midg,midg -2.3772101E-08 1.5498136E-07 gauss-seidel spectral radius is 0.9895973 estimated iterations to convergence 80 setup time was (sec) 0.3700000 now iterating at: 05:49:26 rms-change max change #iterations 0.2019001 29.42807 at 10iterations 2.4832396E-02 3.432781 at 20iterations 3.2005163E-03 0.4296951 at 30iterations 4.8814583E-04 6.6956997E-02 at 40iterations 1.0496515E-04 1.4318466E-02 at 50iterations finished qdiffx linear iterations at : 05:49:29 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.0496515E-04 1.4318466E-02 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 05:49:29 3.347u 0.151s 0:03.90 89.4% 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 Tue Oct 11 2011 at 05:49:29 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 = 2034 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.124190 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): -20.18000 23.80600 ymin,ymax (A): -11.97000 28.73700 zmin,zma (A): -3.482000 46.79600 x,y,z range (A): 43.98600 40.70700 50.27800 scale (grids/A): 2.124190 object centre (A): 1.813000 8.383500 21.65700 number of atom coordinates read : 2034 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 90.50854 89.02119 91.42645 assigned negative charge : -304.2972 centred at (gu) : 89.97312 89.08546 91.50797 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 73548 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16681 grid for indexing accessible points = 1.400000 m= 29457 mr = 52333 m= 5884 mr = 22353 m= 567 mr = 3959 m= 19 mr = 313 m= 0 mr = 4 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 30513 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 79 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 15314 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) : 0.7080632 object centre at (A) : 1.813000 8.383500 21.65700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5259120E-02 6.7995273E-02 midg,1,midg; midg,igrid,midg 3.1678006E-02 4.9232310E-03 1,midg,midg; igrid,midg,midg 1.5316896E-02 4.4116367E-02 gauss-seidel spectral radius is 0.9988278 estimated iterations to convergence 231 setup time was (sec) 0.5800000 now iterating at: 05:49:30 rms-change max change #iterations 4.582037 240.7240 at 10iterations 2.264919 80.32539 at 20iterations 1.123581 35.46600 at 30iterations 0.5557780 17.43556 at 40iterations 0.2767270 8.510927 at 50iterations 0.1374478 4.581558 at 60iterations 6.8300165E-02 2.192101 at 70iterations 3.3882242E-02 1.032651 at 80iterations 1.6804190E-02 0.5148697 at 90iterations 8.3604380E-03 0.2436676 at 100iterations 4.1758073E-03 0.1365747 at 110iterations 2.0931589E-03 6.7492247E-02 at 120iterations finished qdiffx linear iterations at : 05:49:37 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 2.0931589E-03 6.7492247E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 05:49:38 7.725u 0.208s 0:08.37 94.6% 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 Tue Oct 11 2011 at 05:49:38 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 = 2034 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.186284 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): -20.18000 23.80600 ymin,ymax (A): -11.97000 28.73700 zmin,zma (A): -3.482000 46.79600 x,y,z range (A): 43.98600 40.70700 50.27800 scale (grids/A): 3.186284 object centre (A): 1.813000 8.383500 21.65700 number of atom coordinates read : 2034 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 90.76279 88.53171 92.13963 assigned negative charge : -304.2972 centred at (gu) : 89.95964 88.62823 92.26184 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 169753 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16681 grid for indexing accessible points = 1.400000 m= 92022 mr = 126242 m= 37600 mr = 76646 m= 11085 mr = 30974 m= 2268 mr = 8580 m= 270 mr = 1702 m= 9 mr = 181 m= 0 mr = 3 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.150000 number of dielectric boundary points 68679 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 15432 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) : 2.124190 object centre at (A) : 1.813000 8.383500 21.65700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2816049 0.7091550 midg,1,midg; midg,igrid,midg 0.2503610 -2.0818086E-03 1,midg,midg; igrid,midg,midg 0.2537747 0.3081716 gauss-seidel spectral radius is 0.9992928 estimated iterations to convergence 297 setup time was (sec) 1.380000 now iterating at: 05:49:39 rms-change max change #iterations 10.14729 296.1059 at 10iterations 5.986605 151.9439 at 20iterations 3.523692 76.46073 at 30iterations 2.076129 40.36312 at 40iterations 1.221885 22.54091 at 50iterations 0.7176307 15.47747 at 60iterations 0.4207681 7.872277 at 70iterations 0.2464531 4.391876 at 80iterations 0.1443585 2.716370 at 90iterations 8.4177040E-02 1.469120 at 100iterations 4.9389157E-02 0.8623886 at 110iterations 2.9020615E-02 0.5467300 at 120iterations 1.7087935E-02 0.3188419 at 130iterations 1.0158631E-02 0.1852007 at 140iterations 6.1198762E-03 0.1108856 at 150iterations 3.7630305E-03 6.9496155E-02 at 160iterations 2.4131017E-03 5.1277161E-02 at 170iterations 1.6264789E-03 3.1799316E-02 at 180iterations finished qdiffx linear iterations at : 05:49:51 total time elapsed so far: 12.67000 # loops : 180 mean,max change (kT/e) : 1.6264789E-03 3.1799316E-02 energy calculations done at 12.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.79000 DelPhi exited at 05:49:51 12.795u 0.210s 0:13.28 97.8% 0+0k 0+0io 0pf+0w