Sat Oct 15 11:27:30 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 Sat Oct 15 2011 at 11:27:30 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5009 !!! WARNING: FAD 4965 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.2614379 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): -24.31100 75.55400 ymin,ymax (A): -25.78700 95.90200 zmin,zma (A): -23.58200 112.5880 x,y,z range (A): 99.86501 121.6890 136.1700 scale (grids/A): 0.2614379 object centre (A): 25.62150 35.05750 44.50300 number of atom coordinates read : 5009 total number of charged atoms : 4395 net assigned charge : 1.500042 assigned positive charge : 702.1727 centred at (gu) : 84.76210 84.19486 81.08268 assigned negative charge : -700.6762 centred at (gu) : 84.80299 84.23636 81.10822 start vw surface at 0.2000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 1747 nv = 96 ne = 84 npr = 94919 no. pairs analyzed = 94919 no. exposed pairs = 6798 no. arc points = 51322 no. surface atoms = 2305 nbur = 2704 mkacc time = 0.2200000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 3.261440 m= 28 mr = 572 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 1203 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1573 ## 611 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 2249 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7903347E-18 -6.8327835E-22 midg,1,midg; midg,igrid,midg 1.2057117E-18 -4.4833557E-21 1,midg,midg; igrid,midg,midg 8.7885262E-19 -5.7679336E-21 gauss-seidel spectral radius is 0.9278851 estimated iterations to convergence 32 setup time was (sec) 0.7300000 now iterating at: 11:27:31 rms-change max change #iterations 1.7473252E-03 0.7094822 at 10iterations 1.9541485E-04 8.2265854E-02 at 20iterations 2.9042094E-05 1.2800694E-02 at 30iterations 4.3715063E-06 1.9607544E-03 at 40iterations 6.6154360E-07 2.9850006E-04 at 50iterations finished qdiffx linear iterations at : 11:27:35 total time elapsed so far: 4.970000 # loops : 50 mean,max change (kT/e) : 6.6154360E-07 2.9850006E-04 energy calculations done at 4.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.140000 DelPhi exited at 11:27:36 5.144u 0.268s 0:05.89 91.6% 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 Sat Oct 15 2011 at 11:27:36 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5009 !!! WARNING: FAD 4965 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.7843137 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): -24.31100 75.55400 ymin,ymax (A): -25.78700 95.90200 zmin,zma (A): -23.58200 112.5880 x,y,z range (A): 99.86501 121.6890 136.1700 scale (grids/A): 0.7843137 object centre (A): 25.62150 35.05750 44.50300 number of atom coordinates read : 5009 total number of charged atoms : 4395 net assigned charge : 1.500042 assigned positive charge : 702.1727 centred at (gu) : 74.28506 72.58341 63.24677 assigned negative charge : -700.6762 centred at (gu) : 74.40881 72.70879 63.32470 start vw surface at 0.1800000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 22938 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51322 initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 3.028480 m= 2079 mr = 12372 m= 19 mr = 612 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 179 time to turn everything in is 0.3400000 number of dielectric boundary points 12052 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2785 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 20267 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) : 0.2614379 object centre at (A) : 25.62150 35.05750 44.50300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8632869E-04 -7.3304791E-06 midg,1,midg; midg,igrid,midg -1.1313533E-05 -1.4536686E-06 1,midg,midg; igrid,midg,midg 1.6833670E-05 -3.3994849E-07 gauss-seidel spectral radius is 0.9916604 estimated iterations to convergence 89 setup time was (sec) 0.6700000 now iterating at: 11:27:37 rms-change max change #iterations 0.4652418 57.09177 at 10iterations 7.1756586E-02 6.528175 at 20iterations 1.1216989E-02 1.055846 at 30iterations 1.9402957E-03 0.1672201 at 40iterations 5.1789108E-04 4.1084290E-02 at 50iterations 2.0808144E-04 1.5651703E-02 at 60iterations 9.4447256E-05 6.9789886E-03 at 70iterations 4.3368127E-05 3.2224655E-03 at 80iterations 1.9982846E-05 1.4901161E-03 at 90iterations 9.2078863E-06 6.8950653E-04 at 100iterations 4.2484162E-06 3.2138824E-04 at 110iterations 1.9637298E-06 1.4972687E-04 at 120iterations finished qdiffx linear iterations at : 11:27:45 total time elapsed so far: 9.010000 # loops : 120 mean,max change (kT/e) : 1.9637298E-06 1.4972687E-04 energy calculations done at 9.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.190000 DelPhi exited at 11:27:46 9.189u 0.316s 0:10.32 91.9% 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 Sat Oct 15 2011 at 11:27:46 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5009 !!! WARNING: FAD 4965 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.176471 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): -24.31100 75.55400 ymin,ymax (A): -25.78700 95.90200 zmin,zma (A): -23.58200 112.5880 x,y,z range (A): 99.86501 121.6890 136.1700 scale (grids/A): 1.176471 object centre (A): 25.62150 35.05750 44.50300 number of atom coordinates read : 5009 total number of charged atoms : 4395 net assigned charge : 1.500042 assigned positive charge : 702.1727 centred at (gu) : 66.42735 63.87494 49.87008 assigned negative charge : -700.6762 centred at (gu) : 66.61301 64.06319 49.98689 start vw surface at 0.1900000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 55152 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51322 initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.999360 m= 10423 mr = 32893 m= 368 mr = 5673 m= 3 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 566 time to turn everything in is 0.6700000 number of dielectric boundary points 27334 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 918 ## 54 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 28802 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) : 0.7843137 object centre at (A) : 25.62150 35.05750 44.50300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5273114E-02 -4.7314371E-04 midg,1,midg; midg,igrid,midg 1.0089753E-03 -1.0062439E-04 1,midg,midg; igrid,midg,midg 1.7965769E-03 -2.7149888E-05 gauss-seidel spectral radius is 0.9962192 estimated iterations to convergence 130 setup time was (sec) 0.9900000 now iterating at: 11:27:47 rms-change max change #iterations 2.094073 141.1226 at 10iterations 0.6200904 39.23125 at 20iterations 0.1802066 9.668804 at 30iterations 5.2114576E-02 3.390726 at 40iterations 1.5056949E-02 0.7216969 at 50iterations 4.4317557E-03 0.2348614 at 60iterations 1.3939493E-03 6.8241119E-02 at 70iterations 5.3849944E-04 2.6325226E-02 at 80iterations 2.6365183E-04 1.2899399E-02 at 90iterations 1.4991660E-04 7.3776245E-03 at 100iterations 8.9407782E-05 4.2400360E-03 at 110iterations 5.3755692E-05 2.5596619E-03 at 120iterations 3.2419761E-05 1.5487671E-03 at 130iterations 1.9567182E-05 9.4032288E-04 at 140iterations 1.1819538E-05 5.7601929E-04 at 150iterations 7.1477780E-06 3.5858154E-04 at 160iterations 4.3304649E-06 2.1553040E-04 at 170iterations 2.6438199E-06 1.4495850E-04 at 180iterations finished qdiffx linear iterations at : 11:28:00 total time elapsed so far: 13.98000 # loops : 180 mean,max change (kT/e) : 2.6438199E-06 1.4495850E-04 energy calculations done at 13.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.16000 DelPhi exited at 11:28:01 14.164u 0.314s 0:15.21 95.1% 0+0k 0+0io 0pf+0w