Mon Oct 10 16:58:38 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+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 Mon Oct 10 2011 at 16:58:38 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2913 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5302116 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): -34.26100 22.33800 ymin,ymax (A): -45.97500 8.203000 zmin,zma (A): -3.821000 63.32200 x,y,z range (A): 56.59900 54.17800 67.14300 scale (grids/A): 0.5302116 object centre (A): -5.961500 -18.88600 29.75050 number of atom coordinates read : 2913 total number of charged atoms : 2777 net assigned charge : 12.00002 assigned positive charge : 427.0802 centred at (gu) : 89.38908 89.51579 88.65015 assigned negative charge : -415.0809 centred at (gu) : 89.47743 89.58428 88.70518 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5419 nv = 96 ne = 84 npr = 56965 no. pairs analyzed = 56965 no. exposed pairs = 4131 no. arc points = 29436 no. surface atoms = 1381 nbur = 1532 mkacc time = 0.1000000 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= 212 mr = 2445 m= 1 mr = 9 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 0.2400000 number of dielectric boundary points 3178 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3000 ## 437 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 7162 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.0638940E-10 1.4731505E-10 midg,1,midg; midg,igrid,midg 6.9828299E-10 1.3956390E-10 1,midg,midg; igrid,midg,midg 7.9794849E-10 7.7190143E-11 gauss-seidel spectral radius is 0.9816809 estimated iterations to convergence 61 setup time was (sec) 0.4300000 now iterating at: 16:58:39 rms-change max change #iterations 6.1082464E-02 9.781132 at 10iterations 3.6905357E-03 0.6934071 at 20iterations 2.3486761E-04 3.9580822E-02 at 30iterations 1.5336547E-05 2.6421547E-03 at 40iterations 1.2657603E-06 2.1839142E-04 at 50iterations finished qdiffx linear iterations at : 16:58:42 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 1.2657603E-06 2.1839142E-04 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 16:58:42 3.459u 0.183s 0:04.19 86.6% 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 Mon Oct 10 2011 at 16:58:42 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2913 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.590635 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): -34.26100 22.33800 ymin,ymax (A): -45.97500 8.203000 zmin,zma (A): -3.821000 63.32200 x,y,z range (A): 56.59900 54.17800 67.14300 scale (grids/A): 1.590635 object centre (A): -5.961500 -18.88600 29.75050 number of atom coordinates read : 2913 total number of charged atoms : 2777 net assigned charge : 12.00002 assigned positive charge : 427.0802 centred at (gu) : 88.16669 88.54662 85.94974 assigned negative charge : -415.0809 centred at (gu) : 88.43183 88.75214 86.11503 start vw surface at 0.1000000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 60047 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29436 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 16482 mr = 37845 m= 1440 mr = 10174 m= 32 mr = 524 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 613 time to turn everything in is 0.3100000 number of dielectric boundary points 29458 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 420 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 21140 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) : 0.5302116 object centre at (A) : -5.961500 -18.88600 29.75050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3608196E-02 -1.7611753E-02 midg,1,midg; midg,igrid,midg 1.3239601E-02 1.5595412E-03 1,midg,midg; igrid,midg,midg 2.0316496E-02 3.5335671E-03 gauss-seidel spectral radius is 0.9980876 estimated iterations to convergence 182 setup time was (sec) 0.5200000 now iterating at: 16:58:43 rms-change max change #iterations 3.002559 157.9759 at 10iterations 1.218107 49.25370 at 20iterations 0.4926132 19.27468 at 30iterations 0.1994501 7.826569 at 40iterations 8.1298992E-02 3.132965 at 50iterations 3.2923769E-02 1.180460 at 60iterations 1.3393843E-02 0.5521922 at 70iterations 5.4342723E-03 0.2043400 at 80iterations 2.2125447E-03 0.1012955 at 90iterations 9.0086029E-04 3.2646179E-02 at 100iterations 3.6595709E-04 1.4618874E-02 at 110iterations 1.4944510E-04 5.7821274E-03 at 120iterations finished qdiffx linear iterations at : 16:58:50 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 1.4944510E-04 5.7821274E-03 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 16:58:52 7.737u 0.195s 0:09.41 84.1% 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 16:58:52 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2913 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.385952 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): -34.26100 22.33800 ymin,ymax (A): -45.97500 8.203000 zmin,zma (A): -3.821000 63.32200 x,y,z range (A): 56.59900 54.17800 67.14300 scale (grids/A): 2.385952 object centre (A): -5.961500 -18.88600 29.75050 number of atom coordinates read : 2913 total number of charged atoms : 2777 net assigned charge : 12.00002 assigned positive charge : 427.0802 centred at (gu) : 87.24991 87.81978 83.92455 assigned negative charge : -415.0809 centred at (gu) : 87.64761 88.12817 84.17246 start vw surface at 0.1000000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 139662 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29436 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 58448 mr = 93801 m= 14430 mr = 43409 m= 1868 mr = 9852 m= 85 mr = 976 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 1776 time to turn everything in is 0.7300000 number of dielectric boundary points 66438 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 22187 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) : 1.590635 object centre at (A) : -5.961500 -18.88600 29.75050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2311745 -0.3777794 midg,1,midg; midg,igrid,midg 0.1886271 2.5822280E-02 1,midg,midg; igrid,midg,midg 0.3683485 3.9193548E-02 gauss-seidel spectral radius is 0.9991097 estimated iterations to convergence 265 setup time was (sec) 0.9600000 now iterating at: 16:58:53 rms-change max change #iterations 8.080884 300.4252 at 10iterations 4.602528 141.9171 at 20iterations 2.578942 73.61755 at 30iterations 1.429666 41.81741 at 40iterations 0.7919015 22.17165 at 50iterations 0.4368859 10.61966 at 60iterations 0.2396411 5.395065 at 70iterations 0.1312410 2.910938 at 80iterations 7.1936786E-02 1.725576 at 90iterations 3.9293047E-02 0.9271469 at 100iterations 2.1407679E-02 0.4660063 at 110iterations 1.1691711E-02 0.2429905 at 120iterations 6.3687079E-03 0.1343279 at 130iterations 3.4684485E-03 7.7789903E-02 at 140iterations 1.8865967E-03 3.9947510E-02 at 150iterations 1.0315715E-03 2.3667336E-02 at 160iterations 5.6129828E-04 1.2307405E-02 at 170iterations 3.0608944E-04 6.4902306E-03 at 180iterations finished qdiffx linear iterations at : 16:59:04 total time elapsed so far: 12.20000 # loops : 180 mean,max change (kT/e) : 3.0608944E-04 6.4902306E-03 energy calculations done at 12.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.33000 DelPhi exited at 16:59:05 12.336u 0.238s 0:12.89 97.4% 0+0k 0+0io 0pf+0w