Mon Oct 10 14:03:38 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 Mon Oct 10 2011 at 14:03:39 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2878 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: 0.6003271 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): -10.32600 37.36200 ymin,ymax (A): 9.7000003E-02 59.39800 zmin,zma (A): -24.04700 27.93800 x,y,z range (A): 47.68800 59.30100 51.98500 scale (grids/A): 0.6003271 object centre (A): 13.51800 29.74750 1.945500 number of atom coordinates read : 2878 total number of charged atoms : 2499 net assigned charge : 9.500011 assigned positive charge : 388.4413 centred at (gu) : 90.02304 88.77753 89.74783 assigned negative charge : -378.9426 centred at (gu) : 90.11539 88.70034 89.80337 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6514 nv = 96 ne = 84 npr = 51174 no. pairs analyzed = 51174 no. exposed pairs = 3674 no. arc points = 25759 no. surface atoms = 1214 nbur = 1664 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 305 mr = 3294 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 9.0000011E-02 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.2000000 number of dielectric boundary points 3506 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2512 ## 256 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7901 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4834520E-09 2.0260909E-09 midg,1,midg; midg,igrid,midg 1.7087589E-09 5.2525042E-09 1,midg,midg; igrid,midg,midg 7.3904665E-09 7.9247725E-10 gauss-seidel spectral radius is 0.9856511 estimated iterations to convergence 68 setup time was (sec) 0.3700000 now iterating at: 14:03:39 rms-change max change #iterations 0.1060541 16.30508 at 10iterations 9.0005705E-03 1.422024 at 20iterations 7.7637978E-04 0.1074247 at 30iterations 9.1628172E-05 1.4602661E-02 at 40iterations 2.8825432E-05 4.4444799E-03 at 50iterations finished qdiffx linear iterations at : 14:03:42 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 2.8825432E-05 4.4444799E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 14:03:42 3.322u 0.165s 0:03.79 91.8% 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 Mon Oct 10 2011 at 14:03:42 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2878 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: 1.800981 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): -10.32600 37.36200 ymin,ymax (A): 9.7000003E-02 59.39800 zmin,zma (A): -24.04700 27.93800 x,y,z range (A): 47.68800 59.30100 51.98500 scale (grids/A): 1.800981 object centre (A): 13.51800 29.74750 1.945500 number of atom coordinates read : 2878 total number of charged atoms : 2499 net assigned charge : 9.500011 assigned positive charge : 388.4413 centred at (gu) : 90.06830 86.33210 89.24284 assigned negative charge : -378.9426 centred at (gu) : 90.34591 86.10072 89.40977 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70556 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25759 grid for indexing accessible points = 1.400000 m= 24106 mr = 47097 m= 3326 mr = 16800 m= 134 mr = 1821 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 1376 time to turn everything in is 0.3500000 number of dielectric boundary points 32371 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 19333 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) : 0.6003271 object centre at (A) : 13.51800 29.74750 1.945500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7859522E-02 -4.5083072E-03 midg,1,midg; midg,igrid,midg -5.3000386E-04 1.9103710E-02 1,midg,midg; igrid,midg,midg 2.2239521E-02 4.3388340E-03 gauss-seidel spectral radius is 0.9984971 estimated iterations to convergence 205 setup time was (sec) 0.5700000 now iterating at: 14:03:43 rms-change max change #iterations 3.787254 209.3641 at 10iterations 1.710647 64.46748 at 20iterations 0.7720696 26.84700 at 30iterations 0.3486271 11.99181 at 40iterations 0.1573677 5.382219 at 50iterations 7.1320668E-02 2.315278 at 60iterations 3.2267746E-02 1.148036 at 70iterations 1.4537341E-02 0.5031376 at 80iterations 6.5567791E-03 0.2705536 at 90iterations 2.9724757E-03 0.1038046 at 100iterations 1.3419499E-03 4.8073769E-02 at 110iterations 6.0954061E-04 2.1215439E-02 at 120iterations finished qdiffx linear iterations at : 14:03:50 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 6.0954061E-04 2.1215439E-02 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 14:03:51 7.625u 0.177s 0:08.34 93.4% 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 Mon Oct 10 2011 at 14:03:51 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2878 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: 2.701472 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): -10.32600 37.36200 ymin,ymax (A): 9.7000003E-02 59.39800 zmin,zma (A): -24.04700 27.93800 x,y,z range (A): 47.68800 59.30100 51.98500 scale (grids/A): 2.701472 object centre (A): 13.51800 29.74750 1.945500 number of atom coordinates read : 2878 total number of charged atoms : 2499 net assigned charge : 9.500011 assigned positive charge : 388.4413 centred at (gu) : 90.10217 84.49794 88.86391 assigned negative charge : -378.9426 centred at (gu) : 90.51878 84.15103 89.11473 start vw surface at 0.1000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 163099 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25759 grid for indexing accessible points = 1.400000 m= 79026 mr = 115011 m= 26796 mr = 62400 m= 5646 mr = 20560 m= 557 mr = 3889 m= 25 mr = 309 m= 0 mr = 2 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 4776 time to turn everything in is 0.8700000 number of dielectric boundary points 72978 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 19960 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) : 1.800981 object centre at (A) : 13.51800 29.74750 1.945500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4066265 -1.8720575E-02 midg,1,midg; midg,igrid,midg -0.1312852 0.1522465 1,midg,midg; igrid,midg,midg 0.2309192 5.1428128E-02 gauss-seidel spectral radius is 0.9992313 estimated iterations to convergence 285 setup time was (sec) 1.100000 now iterating at: 14:03:52 rms-change max change #iterations 9.164701 326.4520 at 10iterations 5.343529 143.2915 at 20iterations 3.092542 69.36478 at 30iterations 1.783521 41.79562 at 40iterations 1.024973 21.21009 at 50iterations 0.5886302 11.31732 at 60iterations 0.3359403 7.115528 at 70iterations 0.1918981 3.732243 at 80iterations 0.1095833 2.051857 at 90iterations 6.2491156E-02 1.228236 at 100iterations 3.5689116E-02 0.7075632 at 110iterations 2.0292506E-02 0.4035563 at 120iterations 1.1608469E-02 0.2105713 at 130iterations 6.6063222E-03 0.1301041 at 140iterations 3.7519999E-03 7.6799393E-02 at 150iterations 2.1389611E-03 4.1748047E-02 at 160iterations 1.2217321E-03 2.3294449E-02 at 170iterations 7.0127595E-04 1.3179779E-02 at 180iterations finished qdiffx linear iterations at : 14:04:03 total time elapsed so far: 12.18000 # loops : 180 mean,max change (kT/e) : 7.0127595E-04 1.3179779E-02 energy calculations done at 12.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.32000 DelPhi exited at 14:04:04 12.318u 0.200s 0:13.43 93.1% 0+0k 0+0io 0pf+0w