Mon Oct 10 16:03:32 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 16:03:32 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4800 !!! WARNING: GLM 132 has a net charge of -0.0940 !!! WARNING: GLM 134 has a net charge of -0.0940 !!! WARNING: ASP 608 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5400977 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): -19.38700 46.52700 ymin,ymax (A): 8.200999 73.07300 zmin,zma (A): 33.74000 95.33600 x,y,z range (A): 65.91400 64.87200 61.59600 scale (grids/A): 0.5400977 object centre (A): 13.57000 40.63700 64.53799 number of atom coordinates read : 4800 total number of charged atoms : 4633 net assigned charge : 1.812017 assigned positive charge : 723.0966 centred at (gu) : 90.25802 90.94788 89.75996 assigned negative charge : -721.2891 centred at (gu) : 90.23401 90.91909 89.78093 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8872 nv = 96 ne = 84 npr = 99268 no. pairs analyzed = 99268 no. exposed pairs = 5806 no. arc points = 39014 no. surface atoms = 1947 nbur = 2853 mkacc time = 0.2300000 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 = 1.596000 m= 341 mr = 4873 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 4317 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3942 ## 495 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 11818 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8243238E-10 -9.0023697E-11 midg,1,midg; midg,igrid,midg -1.2813783E-10 4.2308893E-10 1,midg,midg; igrid,midg,midg -1.1431467E-10 3.1160979E-10 gauss-seidel spectral radius is 0.9824571 estimated iterations to convergence 62 setup time was (sec) 0.7400000 now iterating at: 16:03:33 rms-change max change #iterations 9.0393372E-02 13.97752 at 10iterations 6.8828925E-03 1.053673 at 20iterations 1.4229374E-03 0.1955948 at 30iterations 5.9563597E-04 7.2261810E-02 at 40iterations 2.7829927E-04 3.4985065E-02 at 50iterations finished qdiffx linear iterations at : 16:03:35 total time elapsed so far: 3.520000 # loops : 50 mean,max change (kT/e) : 2.7829927E-04 3.4985065E-02 energy calculations done at 3.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.710000 DelPhi exited at 16:03:36 3.716u 0.212s 0:04.46 87.8% 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 16:03:36 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4800 !!! WARNING: GLM 132 has a net charge of -0.0940 !!! WARNING: GLM 134 has a net charge of -0.0940 !!! WARNING: ASP 608 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.620293 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): -19.38700 46.52700 ymin,ymax (A): 8.200999 73.07300 zmin,zma (A): 33.74000 95.33600 x,y,z range (A): 65.91400 64.87200 61.59600 scale (grids/A): 1.620293 object centre (A): 13.57000 40.63700 64.53799 number of atom coordinates read : 4800 total number of charged atoms : 4633 net assigned charge : 1.812017 assigned positive charge : 723.0966 centred at (gu) : 90.77246 92.84218 89.27879 assigned negative charge : -721.2891 centred at (gu) : 90.70136 92.75689 89.34241 start vw surface at 0.2100000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 99648 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39014 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 31872 mr = 70976 m= 3416 mr = 22194 m= 79 mr = 1688 m= 0 mr = 11 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 682 time to turn everything in is 0.7400000 number of dielectric boundary points 40146 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 457 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 35397 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) : 0.5400977 object centre at (A) : 13.57000 40.63700 64.53799 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.1761338E-03 9.2685055E-03 midg,1,midg; midg,igrid,midg -4.5020897E-03 -1.4488584E-03 1,midg,midg; igrid,midg,midg -3.4337651E-02 1.0679443E-02 gauss-seidel spectral radius is 0.9983314 estimated iterations to convergence 194 setup time was (sec) 1.040000 now iterating at: 16:03:37 rms-change max change #iterations 4.305607 159.5117 at 10iterations 1.861547 70.38541 at 20iterations 0.8040112 24.37117 at 30iterations 0.3488427 11.09828 at 40iterations 0.1513171 4.482727 at 50iterations 6.5737702E-02 2.047080 at 60iterations 2.8679049E-02 0.8812943 at 70iterations 1.2696154E-02 0.4024439 at 80iterations 5.8636740E-03 0.1991291 at 90iterations 2.9197265E-03 8.7406158E-02 at 100iterations 1.6582427E-03 5.2841187E-02 at 110iterations 1.1019368E-03 3.1806588E-02 at 120iterations finished qdiffx linear iterations at : 16:03:45 total time elapsed so far: 8.270000 # loops : 120 mean,max change (kT/e) : 1.1019368E-03 3.1806588E-02 energy calculations done at 8.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.480000 DelPhi exited at 16:03:45 8.478u 0.243s 0:09.07 96.0% 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 16:03:45 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4800 !!! WARNING: GLM 132 has a net charge of -0.0940 !!! WARNING: GLM 134 has a net charge of -0.0940 !!! WARNING: ASP 608 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.430440 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): -19.38700 46.52700 ymin,ymax (A): 8.200999 73.07300 zmin,zma (A): 33.74000 95.33600 x,y,z range (A): 65.91400 64.87200 61.59600 scale (grids/A): 2.430440 object centre (A): 13.57000 40.63700 64.53799 number of atom coordinates read : 4800 total number of charged atoms : 4633 net assigned charge : 1.812017 assigned positive charge : 723.0966 centred at (gu) : 91.15826 94.26307 88.91781 assigned negative charge : -721.2891 centred at (gu) : 91.05200 94.13523 89.01353 start vw surface at 0.2100000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 232384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39014 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 109667 mr = 173610 m= 32245 mr = 87550 m= 5216 mr = 24475 m= 400 mr = 3482 m= 9 mr = 169 m= 0 mr = 0 time to grow re-entrant surface = 1.080000 no. cavity mid-points inaccessible to solvent = 2265 time to turn everything in is 1.820000 number of dielectric boundary points 90635 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 39 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 37018 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) : 1.620293 object centre at (A) : 13.57000 40.63700 64.53799 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6660881E-02 0.1545720 midg,1,midg; midg,igrid,midg -9.7421698E-02 -1.8980959E-02 1,midg,midg; igrid,midg,midg -0.7263411 0.1778353 gauss-seidel spectral radius is 0.9992217 estimated iterations to convergence 283 setup time was (sec) 2.150000 now iterating at: 16:03:48 rms-change max change #iterations 11.19610 274.4081 at 10iterations 6.558935 148.7357 at 20iterations 3.816028 90.91557 at 30iterations 2.210507 47.16490 at 40iterations 1.274783 28.27530 at 50iterations 0.7340869 14.63080 at 60iterations 0.4213111 8.096846 at 70iterations 0.2414744 4.693853 at 80iterations 0.1381383 2.412918 at 90iterations 7.8897133E-02 1.411903 at 100iterations 4.5125466E-02 0.8205982 at 110iterations 2.5800999E-02 0.4287491 at 120iterations 1.4805847E-02 0.2619286 at 130iterations 8.5474793E-03 0.1837106 at 140iterations 5.0024046E-03 9.1979980E-02 at 150iterations 3.0051090E-03 5.1578522E-02 at 160iterations 1.8885984E-03 3.2609940E-02 at 170iterations 1.2677414E-03 2.0874023E-02 at 180iterations finished qdiffx linear iterations at : 16:03:59 total time elapsed so far: 13.45000 # loops : 180 mean,max change (kT/e) : 1.2677414E-03 2.0874023E-02 energy calculations done at 13.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.65000 DelPhi exited at 16:03:59 13.651u 0.205s 0:14.14 97.9% 0+0k 0+0io 0pf+0w