Tue Oct 11 03:34:26 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 Tue Oct 11 2011 at 03:34:26 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2235 !!! WARNING: ASL 331 has a net charge of -0.1000 !!! WARNING: HIR 435 has a net charge of 0.5140 !!! WARNING: ASP 461 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6442622 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): 22.86000 77.81600 ymin,ymax (A): -5.833000 35.77800 zmin,zma (A): 82.46300 137.7200 x,y,z range (A): 54.95600 41.61100 55.25700 scale (grids/A): 0.6442622 object centre (A): 50.33800 14.97250 110.0915 number of atom coordinates read : 2235 total number of charged atoms : 2129 net assigned charge : -6.585984 assigned positive charge : 330.4804 centred at (gu) : 90.21539 90.22583 90.08839 assigned negative charge : -337.0668 centred at (gu) : 90.00494 90.16406 90.09295 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6208 nv = 96 ne = 84 npr = 46042 no. pairs analyzed = 46042 no. exposed pairs = 2809 no. arc points = 20070 no. surface atoms = 950 nbur = 1285 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 329 mr = 3303 m= 1 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.2700000 number of dielectric boundary points 3188 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1877 ## 142 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7447 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0173821E-08 -1.1604961E-08 midg,1,midg; midg,igrid,midg -1.7122124E-08 -4.0622243E-09 1,midg,midg; igrid,midg,midg -3.3788954E-08 1.3157317E-08 gauss-seidel spectral radius is 0.9874876 estimated iterations to convergence 73 setup time was (sec) 0.4900000 now iterating at: 03:34:27 rms-change max change #iterations 0.1406794 24.65720 at 10iterations 1.3735614E-02 2.053448 at 20iterations 1.3793347E-03 0.2202530 at 30iterations 1.3923482E-04 2.1301270E-02 at 40iterations 1.4014970E-05 2.0637512E-03 at 50iterations finished qdiffx linear iterations at : 03:34:29 total time elapsed so far: 3.000000 # loops : 50 mean,max change (kT/e) : 1.4014970E-05 2.0637512E-03 energy calculations done at 3.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 03:34:30 3.178u 0.191s 0:03.68 91.3% 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 03:34:30 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2235 !!! WARNING: ASL 331 has a net charge of -0.1000 !!! WARNING: HIR 435 has a net charge of 0.5140 !!! WARNING: ASP 461 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.932787 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): 22.86000 77.81600 ymin,ymax (A): -5.833000 35.77800 zmin,zma (A): 82.46300 137.7200 x,y,z range (A): 54.95600 41.61100 55.25700 scale (grids/A): 1.932787 object centre (A): 50.33800 14.97250 110.0915 number of atom coordinates read : 2235 total number of charged atoms : 2129 net assigned charge : -6.585984 assigned positive charge : 330.4804 centred at (gu) : 90.64585 90.67707 90.26497 assigned negative charge : -337.0668 centred at (gu) : 90.01469 90.49216 90.27887 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 66845 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20070 grid for indexing accessible points = 1.400000 m= 23102 mr = 45558 m= 3656 mr = 16613 m= 208 mr = 2192 m= 8 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 318 time to turn everything in is 0.5200000 number of dielectric boundary points 29415 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 91 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 16765 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) : 0.6442622 object centre at (A) : 50.33800 14.97250 110.0915 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4784783E-04 -3.6625717E-02 midg,1,midg; midg,igrid,midg 1.5420074E-03 1.1967033E-02 1,midg,midg; igrid,midg,midg -8.3443515E-02 -4.7971230E-02 gauss-seidel spectral radius is 0.9986413 estimated iterations to convergence 215 setup time was (sec) 0.7900000 now iterating at: 03:34:31 rms-change max change #iterations 4.016654 198.8021 at 10iterations 1.881988 72.18449 at 20iterations 0.8830600 32.52688 at 30iterations 0.4124697 14.78918 at 40iterations 0.1936709 6.795664 at 50iterations 9.0482853E-02 2.965873 at 60iterations 4.2384621E-02 1.402716 at 70iterations 1.9925201E-02 0.6935208 at 80iterations 9.3280245E-03 0.2957478 at 90iterations 4.3810657E-03 0.1453476 at 100iterations 2.0567223E-03 8.2192898E-02 at 110iterations 9.6224062E-04 3.2585621E-02 at 120iterations finished qdiffx linear iterations at : 03:34:38 total time elapsed so far: 7.350000 # loops : 120 mean,max change (kT/e) : 9.6224062E-04 3.2585621E-02 energy calculations done at 7.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.530000 DelPhi exited at 03:34:38 7.529u 0.227s 0:08.09 95.6% 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 Tue Oct 11 2011 at 03:34:38 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2235 !!! WARNING: ASL 331 has a net charge of -0.1000 !!! WARNING: HIR 435 has a net charge of 0.5140 !!! WARNING: ASP 461 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.899180 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): 22.86000 77.81600 ymin,ymax (A): -5.833000 35.77800 zmin,zma (A): 82.46300 137.7200 x,y,z range (A): 54.95600 41.61100 55.25700 scale (grids/A): 2.899180 object centre (A): 50.33800 14.97250 110.0915 number of atom coordinates read : 2235 total number of charged atoms : 2129 net assigned charge : -6.585984 assigned positive charge : 330.4804 centred at (gu) : 90.96872 91.01550 90.39729 assigned negative charge : -337.0668 centred at (gu) : 90.02204 90.73820 90.41821 start vw surface at 0.1400000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 154595 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20070 grid for indexing accessible points = 1.400000 m= 74592 mr = 110553 m= 27154 mr = 60111 m= 6533 mr = 21480 m= 892 mr = 4731 m= 54 mr = 567 m= 3 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 1100 time to turn everything in is 1.190000 number of dielectric boundary points 66364 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 17032 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) : 1.932787 object centre at (A) : 50.33800 14.97250 110.0915 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8566463E-02 -0.4049802 midg,1,midg; midg,igrid,midg 3.0264957E-02 0.1296406 1,midg,midg; igrid,midg,midg -0.9755247 -0.4585495 gauss-seidel spectral radius is 0.9992597 estimated iterations to convergence 290 setup time was (sec) 1.480000 now iterating at: 03:34:40 rms-change max change #iterations 9.361318 339.3148 at 10iterations 5.418423 126.3689 at 20iterations 3.130334 66.38589 at 30iterations 1.797260 37.28750 at 40iterations 1.033246 21.42971 at 50iterations 0.5963538 11.25566 at 60iterations 0.3413709 6.739062 at 70iterations 0.1957810 3.640280 at 80iterations 0.1123545 2.119759 at 90iterations 6.4474538E-02 1.229206 at 100iterations 3.7032187E-02 0.6731787 at 110iterations 2.1250617E-02 0.4370089 at 120iterations 1.2168249E-02 0.2436409 at 130iterations 6.9705318E-03 0.1240110 at 140iterations 4.0022056E-03 7.4275970E-02 at 150iterations 2.2967453E-03 4.6495914E-02 at 160iterations 1.3153665E-03 2.4261475E-02 at 170iterations 7.5551565E-04 1.5174866E-02 at 180iterations finished qdiffx linear iterations at : 03:34:50 total time elapsed so far: 11.76000 # loops : 180 mean,max change (kT/e) : 7.5551565E-04 1.5174866E-02 energy calculations done at 11.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.97000 DelPhi exited at 03:34:51 11.974u 0.228s 0:12.51 97.4% 0+0k 0+0io 0pf+0w