Sat Oct 15 14:29:33 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 14:29:33 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 = 2904 !!! WARNING: ASP 354 has a net charge of -0.5000 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: 0.6059059 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): -27.24500 31.51000 ymin,ymax (A): -10.28800 39.52400 zmin,zma (A): 6.416000 61.40600 x,y,z range (A): 58.75500 49.81200 54.99000 scale (grids/A): 0.6059059 object centre (A): 2.132501 14.61800 33.91100 number of atom coordinates read : 2904 total number of charged atoms : 2763 net assigned charge : -4.499967 assigned positive charge : 437.4051 centred at (gu) : 91.31384 90.47434 91.06096 assigned negative charge : -441.9063 centred at (gu) : 91.41399 90.34901 91.16488 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7068 nv = 96 ne = 84 npr = 58346 no. pairs analyzed = 58346 no. exposed pairs = 3775 no. arc points = 26740 no. surface atoms = 1265 nbur = 1639 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 333 mr = 3657 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.3500000 number of dielectric boundary points 3725 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2709 ## 277 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8876 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2414386E-09 -9.4583292E-09 midg,1,midg; midg,igrid,midg -7.6589188E-09 4.3827804E-09 1,midg,midg; igrid,midg,midg 1.9766506E-09 -9.7633057E-09 gauss-seidel spectral radius is 0.9859288 estimated iterations to convergence 69 setup time was (sec) 0.7000000 now iterating at: 14:29:35 rms-change max change #iterations 0.1196947 20.63361 at 10iterations 1.0365540E-02 1.372212 at 20iterations 9.0788159E-04 0.1242037 at 30iterations 8.0413745E-05 1.4427185E-02 at 40iterations 7.2257440E-06 1.0528564E-03 at 50iterations finished qdiffx linear iterations at : 14:29:40 total time elapsed so far: 5.300000 # loops : 50 mean,max change (kT/e) : 7.2257440E-06 1.0528564E-03 energy calculations done at 5.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.470000 DelPhi exited at 14:29:41 5.474u 0.460s 0:07.77 76.3% 0+0k 0+0io 5pf+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 14:29:42 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 = 2904 !!! WARNING: ASP 354 has a net charge of -0.5000 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: 1.817718 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): -27.24500 31.51000 ymin,ymax (A): -10.28800 39.52400 zmin,zma (A): 6.416000 61.40600 x,y,z range (A): 58.75500 49.81200 54.99000 scale (grids/A): 1.817718 object centre (A): 2.132501 14.61800 33.91100 number of atom coordinates read : 2904 total number of charged atoms : 2763 net assigned charge : -4.499967 assigned positive charge : 437.4051 centred at (gu) : 93.94073 91.42191 93.18216 assigned negative charge : -441.9063 centred at (gu) : 94.24127 91.04650 93.49408 start vw surface at 0.1200000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 77229 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26740 grid for indexing accessible points = 1.400000 m= 25497 mr = 52397 m= 3307 mr = 17761 m= 160 mr = 1756 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 841 time to turn everything in is 0.6300000 number of dielectric boundary points 34253 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 222 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 21635 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) : 0.6059059 object centre at (A) : 2.132501 14.61800 33.91100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.7217085E-03 -5.3800149E-03 midg,1,midg; midg,igrid,midg -2.1275187E-02 4.7258087E-03 1,midg,midg; igrid,midg,midg 2.6877224E-02 -5.6220751E-02 gauss-seidel spectral radius is 0.9985383 estimated iterations to convergence 207 setup time was (sec) 0.9800000 now iterating at: 14:29:44 rms-change max change #iterations 4.146900 180.7983 at 10iterations 1.874503 67.13078 at 20iterations 0.8549981 27.45965 at 30iterations 0.3890795 12.70144 at 40iterations 0.1766906 5.865118 at 50iterations 8.0519766E-02 2.608809 at 60iterations 3.6670342E-02 1.193697 at 70iterations 1.6743472E-02 0.5992994 at 80iterations 7.6321536E-03 0.2274637 at 90iterations 3.4714374E-03 0.1060028 at 100iterations 1.5909382E-03 5.3558350E-02 at 110iterations 7.2433351E-04 2.4934769E-02 at 120iterations finished qdiffx linear iterations at : 14:30:10 total time elapsed so far: 12.73000 # loops : 120 mean,max change (kT/e) : 7.2433351E-04 2.4934769E-02 energy calculations done at 12.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 14:30:12 12.905u 0.563s 0:29.45 45.7% 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 Sat Oct 15 2011 at 14:30:12 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 = 2904 !!! WARNING: ASP 354 has a net charge of -0.5000 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: 2.726577 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): -27.24500 31.51000 ymin,ymax (A): -10.28800 39.52400 zmin,zma (A): 6.416000 61.40600 x,y,z range (A): 58.75500 49.81200 54.99000 scale (grids/A): 2.726577 object centre (A): 2.132501 14.61800 33.91100 number of atom coordinates read : 2904 total number of charged atoms : 2763 net assigned charge : -4.499967 assigned positive charge : 437.4051 centred at (gu) : 95.91080 92.13277 94.77295 assigned negative charge : -441.9063 centred at (gu) : 96.36179 91.56973 95.24119 start vw surface at 0.1500000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 178916 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26740 grid for indexing accessible points = 1.400000 m= 85466 mr = 127793 m= 27375 mr = 67876 m= 5353 mr = 20875 m= 622 mr = 3543 m= 21 mr = 359 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 2835 time to turn everything in is 1.710000 number of dielectric boundary points 77302 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.890000 number of grid points assigned charge 22099 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) : 1.817718 object centre at (A) : 2.132501 14.61800 33.91100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6226826E-03 0.1295037 midg,1,midg; midg,igrid,midg -0.2294866 7.3885962E-02 1,midg,midg; igrid,midg,midg 0.3813489 -0.6287680 gauss-seidel spectral radius is 0.9992484 estimated iterations to convergence 288 setup time was (sec) 2.130000 now iterating at: 14:30:20 rms-change max change #iterations 10.15904 336.5333 at 10iterations 5.980661 165.4882 at 20iterations 3.495277 80.58826 at 30iterations 2.028883 51.94836 at 40iterations 1.172421 26.09930 at 50iterations 0.6776065 12.39647 at 60iterations 0.3892674 8.031368 at 70iterations 0.2242265 4.643896 at 80iterations 0.1289718 2.298761 at 90iterations 7.3960274E-02 1.416124 at 100iterations 4.2390816E-02 0.7539406 at 110iterations 2.4347441E-02 0.4799862 at 120iterations 1.3911052E-02 0.2656822 at 130iterations 7.9703275E-03 0.1449814 at 140iterations 4.5663803E-03 8.7789536E-02 at 150iterations 2.6127093E-03 5.7968140E-02 at 160iterations 1.4944179E-03 3.0952215E-02 at 170iterations 8.5745181E-04 1.6780853E-02 at 180iterations finished qdiffx linear iterations at : 14:31:01 total time elapsed so far: 22.18000 # loops : 180 mean,max change (kT/e) : 8.5745181E-04 1.6780853E-02 energy calculations done at 22.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.34000 DelPhi exited at 14:31:03 22.349u 0.623s 0:51.13 44.9% 0+0k 0+0io 0pf+0w