Tue Oct 11 06:49:04 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 06:49:04 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 = 2954 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5566589 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): -18.42700 45.52600 ymin,ymax (A): 21.54200 78.69500 zmin,zma (A): -72.27100 -23.16800 x,y,z range (A): 63.95300 57.15300 49.10300 scale (grids/A): 0.5566589 object centre (A): 13.54950 50.11850 -47.71950 number of atom coordinates read : 2954 total number of charged atoms : 2814 net assigned charge : -1.999989 assigned positive charge : 430.5746 centred at (gu) : 88.91788 89.73232 90.01854 assigned negative charge : -432.5753 centred at (gu) : 88.89719 89.82137 90.01038 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 5923 nv = 96 ne = 84 npr = 61018 no. pairs analyzed = 61018 no. exposed pairs = 3675 no. arc points = 25742 no. surface atoms = 1243 nbur = 1711 mkacc time = 0.1300000 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 = 1.540000 m= 230 mr = 3143 m= 0 mr = 20 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.3700000 number of dielectric boundary points 2990 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2541 ## 317 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7706 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6417027E-10 -1.0986361E-10 midg,1,midg; midg,igrid,midg 7.0027800E-10 -9.8158359E-10 1,midg,midg; igrid,midg,midg -5.0183008E-10 5.8544814E-12 gauss-seidel spectral radius is 0.9833546 estimated iterations to convergence 64 setup time was (sec) 0.5800000 now iterating at: 06:49:05 rms-change max change #iterations 7.9603881E-02 11.90527 at 10iterations 5.6022406E-03 0.8874264 at 20iterations 4.1695355E-04 7.1891785E-02 at 30iterations 4.4746830E-05 1.0501862E-02 at 40iterations 8.1865537E-06 2.0294189E-03 at 50iterations finished qdiffx linear iterations at : 06:49:07 total time elapsed so far: 2.980000 # loops : 50 mean,max change (kT/e) : 8.1865537E-06 2.0294189E-03 energy calculations done at 2.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 06:49:08 3.147u 0.158s 0:03.66 89.8% 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 Tue Oct 11 2011 at 06:49:08 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 = 2954 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.669976 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): -18.42700 45.52600 ymin,ymax (A): 21.54200 78.69500 zmin,zma (A): -72.27100 -23.16800 x,y,z range (A): 63.95300 57.15300 49.10300 scale (grids/A): 1.669976 object centre (A): 13.54950 50.11850 -47.71950 number of atom coordinates read : 2954 total number of charged atoms : 2814 net assigned charge : -1.999989 assigned positive charge : 430.5746 centred at (gu) : 86.75278 89.19635 90.05519 assigned negative charge : -432.5753 centred at (gu) : 86.69147 89.46376 90.03044 start vw surface at 0.2000000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 65936 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25742 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 20833 mr = 45019 m= 2279 mr = 14818 m= 54 mr = 1285 m= 0 mr = 9 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1199 time to turn everything in is 0.5000000 number of dielectric boundary points 27971 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 241 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 21652 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) : 0.5566589 object centre at (A) : 13.54950 50.11850 -47.71950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9393356E-03 9.8543167E-03 midg,1,midg; midg,igrid,midg -1.4538667E-03 6.3695023E-03 1,midg,midg; igrid,midg,midg -1.6545976E-02 -3.1770274E-02 gauss-seidel spectral radius is 0.9982665 estimated iterations to convergence 191 setup time was (sec) 0.7900000 now iterating at: 06:49:09 rms-change max change #iterations 3.411334 150.1301 at 10iterations 1.451252 58.45788 at 20iterations 0.6166456 23.99054 at 30iterations 0.2623409 9.057877 at 40iterations 0.1122027 4.049212 at 50iterations 4.7751911E-02 1.659363 at 60iterations 2.0221639E-02 0.6669865 at 70iterations 8.6136721E-03 0.2770863 at 80iterations 3.6797763E-03 0.1290855 at 90iterations 1.5653939E-03 5.4059982E-02 at 100iterations 6.6790171E-04 2.4929047E-02 at 110iterations 2.8544397E-04 1.0452271E-02 at 120iterations finished qdiffx linear iterations at : 06:49:15 total time elapsed so far: 7.140000 # loops : 120 mean,max change (kT/e) : 2.8544397E-04 1.0452271E-02 energy calculations done at 7.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.320000 DelPhi exited at 06:49:16 7.321u 0.195s 0:08.21 91.4% 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 06:49:16 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 = 2954 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.504965 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): -18.42700 45.52600 ymin,ymax (A): 21.54200 78.69500 zmin,zma (A): -72.27100 -23.16800 x,y,z range (A): 63.95300 57.15300 49.10300 scale (grids/A): 2.504965 object centre (A): 13.54950 50.11850 -47.71950 number of atom coordinates read : 2954 total number of charged atoms : 2814 net assigned charge : -1.999989 assigned positive charge : 430.5746 centred at (gu) : 85.12907 88.79447 90.08286 assigned negative charge : -432.5753 centred at (gu) : 85.03710 89.19573 90.04572 start vw surface at 0.1500000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 152872 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25742 grid for indexing accessible points = 1.400000 m= 71444 mr = 109767 m= 21322 mr = 57483 m= 3688 mr = 16591 m= 302 mr = 2655 m= 5 mr = 146 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 4085 time to turn everything in is 1.070000 number of dielectric boundary points 62991 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 22497 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) : 1.669976 object centre at (A) : 13.54950 50.11850 -47.71950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1009519 0.1606416 midg,1,midg; midg,igrid,midg -2.7669033E-02 0.1280019 1,midg,midg; igrid,midg,midg -0.2537514 -0.7944604 gauss-seidel spectral radius is 0.9991646 estimated iterations to convergence 273 setup time was (sec) 1.350000 now iterating at: 06:49:17 rms-change max change #iterations 8.712357 282.5237 at 10iterations 4.896956 110.6758 at 20iterations 2.753116 63.70651 at 30iterations 1.543985 31.93515 at 40iterations 0.8603451 17.62106 at 50iterations 0.4806306 10.17029 at 60iterations 0.2667561 5.471577 at 70iterations 0.1486763 3.274195 at 80iterations 8.2515672E-02 1.601231 at 90iterations 4.5744751E-02 0.9453039 at 100iterations 2.5349295E-02 0.5334053 at 110iterations 1.4050631E-02 0.2764807 at 120iterations 7.8102150E-03 0.1679783 at 130iterations 4.3343427E-03 8.6968064E-02 at 140iterations 2.4039485E-03 5.3552628E-02 at 150iterations 1.3341235E-03 2.8068542E-02 at 160iterations 7.4111536E-04 1.4761448E-02 at 170iterations 4.1161667E-04 8.6059570E-03 at 180iterations finished qdiffx linear iterations at : 06:49:27 total time elapsed so far: 10.48000 # loops : 180 mean,max change (kT/e) : 4.1161667E-04 8.6059570E-03 energy calculations done at 10.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.65000 DelPhi exited at 06:49:27 10.657u 0.150s 0:11.27 95.8% 0+0k 0+0io 0pf+0w