Tue Oct 11 03:40:59 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 03:40:59 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3175 !!! WARNING: HIZ 79 has a net charge of 0.2000 !!! WARNING: ZN3 300 has a net charge of 1.4000 !!! WARNING: ZN3 301 has a net charge of 1.4000 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6056585 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): -11.06100 37.04700 ymin,ymax (A): -27.16300 21.14100 zmin,zma (A): -13.27000 45.50900 x,y,z range (A): 48.10800 48.30400 58.77900 scale (grids/A): 0.6056585 object centre (A): 12.99300 -3.011001 16.11950 number of atom coordinates read : 3175 total number of charged atoms : 2761 net assigned charge : 1.662023 assigned positive charge : 444.4904 centred at (gu) : 89.98242 90.83951 92.38511 assigned negative charge : -442.8291 centred at (gu) : 89.74619 90.77991 92.27589 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7016 nv = 96 ne = 84 npr = 59407 no. pairs analyzed = 59407 no. exposed pairs = 3438 no. arc points = 23881 no. surface atoms = 1162 nbur = 2013 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 346 mr = 3953 m= 4 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 47 time to turn everything in is 0.3900000 number of dielectric boundary points 3361 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2463 ## 286 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8771 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7521221E-09 1.0418645E-08 midg,1,midg; midg,igrid,midg -1.8542793E-09 4.3715747E-09 1,midg,midg; igrid,midg,midg -1.1291521E-08 1.1964954E-08 gauss-seidel spectral radius is 0.9859103 estimated iterations to convergence 69 setup time was (sec) 0.6600000 now iterating at: 03:41:00 rms-change max change #iterations 0.1258986 18.91475 at 10iterations 1.0854674E-02 1.649731 at 20iterations 1.0011429E-03 0.1440611 at 30iterations 1.2764079E-04 2.1320343E-02 at 40iterations 2.9954803E-05 5.7926178E-03 at 50iterations finished qdiffx linear iterations at : 03:41:03 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 2.9954803E-05 5.7926178E-03 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.180000 DelPhi exited at 03:41:04 4.182u 0.268s 0:04.95 89.6% 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 03:41:04 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3175 !!! WARNING: HIZ 79 has a net charge of 0.2000 !!! WARNING: ZN3 300 has a net charge of 1.4000 !!! WARNING: ZN3 301 has a net charge of 1.4000 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.816975 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): -11.06100 37.04700 ymin,ymax (A): -27.16300 21.14100 zmin,zma (A): -13.27000 45.50900 x,y,z range (A): 48.10800 48.30400 58.77900 scale (grids/A): 1.816975 object centre (A): 12.99300 -3.011001 16.11950 number of atom coordinates read : 3175 total number of charged atoms : 2761 net assigned charge : 1.662023 assigned positive charge : 444.4904 centred at (gu) : 89.94648 92.51775 97.15485 assigned negative charge : -442.8291 centred at (gu) : 89.23818 92.33918 96.82726 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 76345 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23881 grid for indexing accessible points = 1.400000 m= 27647 mr = 53933 m= 3992 mr = 20685 m= 191 mr = 2443 m= 1 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1838 time to turn everything in is 0.6700000 number of dielectric boundary points 31048 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 206 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 21541 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) : 0.6056585 object centre at (A) : 12.99300 -3.011001 16.11950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4394342E-02 5.1720547E-03 midg,1,midg; midg,igrid,midg 3.8856214E-03 2.6269802E-03 1,midg,midg; igrid,midg,midg -8.3096977E-03 3.9109942E-02 gauss-seidel spectral radius is 0.9985297 estimated iterations to convergence 207 setup time was (sec) 0.9700000 now iterating at: 03:41:05 rms-change max change #iterations 4.201602 243.6832 at 10iterations 1.913404 71.61294 at 20iterations 0.8698993 30.94318 at 30iterations 0.3973897 12.65965 at 40iterations 0.1815166 5.733933 at 50iterations 8.2707323E-02 2.953823 at 60iterations 3.7768967E-02 1.226131 at 70iterations 1.7280981E-02 0.5606956 at 80iterations 7.8854179E-03 0.2353630 at 90iterations 3.6059599E-03 0.1183681 at 100iterations 1.6561265E-03 5.5442810E-02 at 110iterations 7.6527003E-04 2.6740074E-02 at 120iterations finished qdiffx linear iterations at : 03:41:14 total time elapsed so far: 9.420000 # loops : 120 mean,max change (kT/e) : 7.6527003E-04 2.6740074E-02 energy calculations done at 9.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.610000 DelPhi exited at 03:41:15 9.613u 0.318s 0:10.47 94.7% 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 Tue Oct 11 2011 at 03:41:15 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3175 !!! WARNING: HIZ 79 has a net charge of 0.2000 !!! WARNING: ZN3 300 has a net charge of 1.4000 !!! WARNING: ZN3 301 has a net charge of 1.4000 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.725463 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): -11.06100 37.04700 ymin,ymax (A): -27.16300 21.14100 zmin,zma (A): -13.27000 45.50900 x,y,z range (A): 48.10800 48.30400 58.77900 scale (grids/A): 2.725463 object centre (A): 12.99300 -3.011001 16.11950 number of atom coordinates read : 3175 total number of charged atoms : 2761 net assigned charge : 1.662023 assigned positive charge : 444.4904 centred at (gu) : 89.91961 93.77663 100.7320 assigned negative charge : -442.8291 centred at (gu) : 88.85706 93.50877 100.2408 start vw surface at 0.1700000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 176550 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23881 grid for indexing accessible points = 1.400000 m= 90452 mr = 130497 m= 32268 mr = 74815 m= 7026 mr = 26103 m= 797 mr = 5284 m= 32 mr = 486 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 6227 time to turn everything in is 1.720000 number of dielectric boundary points 69936 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 22079 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) : 1.816975 object centre at (A) : 12.99300 -3.011001 16.11950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.053604 0.2381062 midg,1,midg; midg,igrid,midg 3.6757149E-02 -4.4435576E-02 1,midg,midg; igrid,midg,midg -7.7883020E-02 0.3860246 gauss-seidel spectral radius is 0.9992298 estimated iterations to convergence 284 setup time was (sec) 2.060000 now iterating at: 03:41:17 rms-change max change #iterations 10.04836 280.9615 at 10iterations 5.802510 140.1580 at 20iterations 3.330059 69.19234 at 30iterations 1.909521 37.51976 at 40iterations 1.091872 22.24820 at 50iterations 0.6242631 11.41397 at 60iterations 0.3559383 6.930299 at 70iterations 0.2031887 3.480759 at 80iterations 0.1158024 2.650700 at 90iterations 6.6146560E-02 1.215439 at 100iterations 3.7651736E-02 0.6434479 at 110iterations 2.1441905E-02 0.4068012 at 120iterations 1.2185573E-02 0.2056189 at 130iterations 6.9538252E-03 0.1207151 at 140iterations 3.9645946E-03 7.7006340E-02 at 150iterations 2.2681621E-03 4.1055679E-02 at 160iterations 1.2980909E-03 2.3387909E-02 at 170iterations 7.4665522E-04 1.3216019E-02 at 180iterations finished qdiffx linear iterations at : 03:41:31 total time elapsed so far: 16.02000 # loops : 180 mean,max change (kT/e) : 7.4665522E-04 1.3216019E-02 energy calculations done at 16.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.20000 DelPhi exited at 03:41:32 16.198u 0.343s 0:17.54 94.2% 0+0k 0+0io 0pf+0w