Mon Oct 10 19:43:10 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 19:43:11 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 = 2800 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: 0.6197664 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): -32.23800 25.20300 ymin,ymax (A): 29.11200 82.65700 zmin,zma (A): 60.40100 108.6180 x,y,z range (A): 57.44100 53.54500 48.21701 scale (grids/A): 0.6197664 object centre (A): -3.517500 55.88450 84.50950 number of atom coordinates read : 2800 total number of charged atoms : 2659 net assigned charge : 3.000029 assigned positive charge : 420.5854 centred at (gu) : 88.46486 91.82765 90.16312 assigned negative charge : -417.5866 centred at (gu) : 88.53848 91.86916 90.20412 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7005 nv = 96 ne = 84 npr = 58120 no. pairs analyzed = 58120 no. exposed pairs = 3466 no. arc points = 24432 no. surface atoms = 1167 nbur = 1633 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 365 mr = 3759 m= 0 mr = 32 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.4100000 number of dielectric boundary points 3579 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2442 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8680 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0585642E-09 -5.7146626E-10 midg,1,midg; midg,igrid,midg 3.5512600E-09 -9.6164199E-10 1,midg,midg; igrid,midg,midg 1.0582174E-08 -2.0144528E-09 gauss-seidel spectral radius is 0.9865332 estimated iterations to convergence 71 setup time was (sec) 0.6900000 now iterating at: 19:43:12 rms-change max change #iterations 0.1282641 18.89060 at 10iterations 1.1707318E-02 1.706353 at 20iterations 1.0784367E-03 0.1471996 at 30iterations 9.9118442E-05 1.3885498E-02 at 40iterations 9.5364949E-06 1.4135838E-03 at 50iterations finished qdiffx linear iterations at : 19:43:15 total time elapsed so far: 4.470000 # loops : 50 mean,max change (kT/e) : 9.5364949E-06 1.4135838E-03 energy calculations done at 4.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.680000 DelPhi exited at 19:43:16 4.689u 0.409s 0:05.48 92.7% 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 19:43:16 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 = 2800 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: 1.859299 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): -32.23800 25.20300 ymin,ymax (A): 29.11200 82.65700 zmin,zma (A): 60.40100 108.6180 x,y,z range (A): 57.44100 53.54500 48.21701 scale (grids/A): 1.859299 object centre (A): -3.517500 55.88450 84.50950 number of atom coordinates read : 2800 total number of charged atoms : 2659 net assigned charge : 3.000029 assigned positive charge : 420.5854 centred at (gu) : 85.39375 95.48219 90.48868 assigned negative charge : -417.5866 centred at (gu) : 85.61517 95.60698 90.61210 start vw surface at 0.1600000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 75618 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24432 grid for indexing accessible points = 1.400000 m= 26806 mr = 51956 m= 4440 mr = 19264 m= 305 mr = 2662 m= 6 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 316 time to turn everything in is 0.7800000 number of dielectric boundary points 33190 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 184 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 20853 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) : 0.6197664 object centre at (A) : -3.517500 55.88450 84.50950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.5285922E-03 6.2168199E-03 midg,1,midg; midg,igrid,midg 1.1705931E-02 -5.8374628E-03 1,midg,midg; igrid,midg,midg 1.4404601E-02 7.5922613E-03 gauss-seidel spectral radius is 0.9985852 estimated iterations to convergence 211 setup time was (sec) 1.090000 now iterating at: 19:43:18 rms-change max change #iterations 4.211595 171.6344 at 10iterations 1.942555 78.00294 at 20iterations 0.8956471 30.20029 at 30iterations 0.4151884 13.08795 at 40iterations 0.1918823 6.256779 at 50iterations 8.8622876E-02 3.087799 at 60iterations 4.0976301E-02 1.394184 at 70iterations 1.8952014E-02 0.5973377 at 80iterations 8.7612513E-03 0.2909136 at 90iterations 4.0472988E-03 0.1296635 at 100iterations 1.8769756E-03 5.8918238E-02 at 110iterations 8.6648663E-04 2.6092529E-02 at 120iterations finished qdiffx linear iterations at : 19:43:27 total time elapsed so far: 10.89000 # loops : 120 mean,max change (kT/e) : 8.6648663E-04 2.6092529E-02 energy calculations done at 10.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.10000 DelPhi exited at 19:43:28 11.109u 0.455s 0:12.13 95.2% 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 19:43:28 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2800 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: 2.788949 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): -32.23800 25.20300 ymin,ymax (A): 29.11200 82.65700 zmin,zma (A): 60.40100 108.6180 x,y,z range (A): 57.44100 53.54500 48.21701 scale (grids/A): 2.788949 object centre (A): -3.517500 55.88450 84.50950 number of atom coordinates read : 2800 total number of charged atoms : 2659 net assigned charge : 3.000029 assigned positive charge : 420.5854 centred at (gu) : 83.09058 98.22318 90.73275 assigned negative charge : -417.5866 centred at (gu) : 83.42277 98.41039 90.91809 start vw surface at 0.1500000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 175572 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24432 grid for indexing accessible points = 1.400000 m= 85895 mr = 126833 m= 31568 mr = 69088 m= 7897 mr = 24770 m= 1149 mr = 5749 m= 59 mr = 727 m= 2 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 1.230000 no. cavity mid-points inaccessible to solvent = 1071 time to turn everything in is 2.020000 number of dielectric boundary points 74956 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.170000 number of grid points assigned charge 21272 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) : 1.859299 object centre at (A) : -3.517500 55.88450 84.50950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.8032173E-02 5.3656962E-02 midg,1,midg; midg,igrid,midg 0.1970664 -0.1122372 1,midg,midg; igrid,midg,midg 9.4774336E-02 7.7443600E-02 gauss-seidel spectral radius is 0.9992512 estimated iterations to convergence 288 setup time was (sec) 2.380000 now iterating at: 19:43:31 rms-change max change #iterations 9.953458 368.0770 at 10iterations 5.794208 120.5100 at 20iterations 3.356784 88.32204 at 30iterations 1.931117 38.63147 at 40iterations 1.111948 22.02479 at 50iterations 0.6391019 11.64490 at 60iterations 0.3667904 6.553033 at 70iterations 0.2109880 3.901855 at 80iterations 0.1210697 2.151839 at 90iterations 6.9408923E-02 1.358736 at 100iterations 3.9696932E-02 0.6920013 at 110iterations 2.2729047E-02 0.4246845 at 120iterations 1.3026932E-02 0.2269869 at 130iterations 7.4574347E-03 0.1381416 at 140iterations 4.2774035E-03 7.5286865E-02 at 150iterations 2.4464603E-03 4.4000566E-02 at 160iterations 1.4026839E-03 2.5912046E-02 at 170iterations 8.0359250E-04 1.5196085E-02 at 180iterations finished qdiffx linear iterations at : 19:43:47 total time elapsed so far: 18.31000 # loops : 180 mean,max change (kT/e) : 8.0359250E-04 1.5196085E-02 energy calculations done at 18.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.52000 DelPhi exited at 19:43:48 18.528u 0.505s 0:19.50 97.5% 0+0k 0+0io 0pf+0w