Sun Oct 9 22:10:26 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 Sun Oct 9 2011 at 22:10:26 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3253 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: SEP 139 has a net charge of -0.4750 !!! WARNING: GLM 422 has a net charge of -0.6000 !!! WARNING: GLM 556 has a net charge of -0.6000 !!! WARNING: ZN7 776 has a net charge of 1.4000 !!! WARNING: ZN7 780 has a net charge of 1.4000 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: 0.6330127 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): 45.37700 98.40100 ymin,ymax (A): 2.955000 59.19400 zmin,zma (A): 14.90500 67.37600 x,y,z range (A): 53.02400 56.23900 52.47100 scale (grids/A): 0.6330127 object centre (A): 71.88900 31.07450 41.14050 number of atom coordinates read : 3253 total number of charged atoms : 3101 net assigned charge : 6.725008 assigned positive charge : 496.5906 centred at (gu) : 90.40239 88.09042 90.48639 assigned negative charge : -489.8671 centred at (gu) : 90.33591 88.04510 90.48866 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8801 nv = 96 ne = 84 npr = 64087 no. pairs analyzed = 64087 no. exposed pairs = 4086 no. arc points = 29689 no. surface atoms = 1380 nbur = 1873 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 435 mr = 4663 m= 4 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.2400000 number of dielectric boundary points 4528 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2996 ## 309 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 10701 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.5164541E-09 8.6022798E-09 midg,1,midg; midg,igrid,midg 3.6066894E-09 9.0209769E-09 1,midg,midg; igrid,midg,midg -1.3376280E-11 1.7473587E-08 gauss-seidel spectral radius is 0.9871379 estimated iterations to convergence 72 setup time was (sec) 0.4300000 now iterating at: 22:10:27 rms-change max change #iterations 0.1599351 24.63524 at 10iterations 1.5305935E-02 1.992208 at 20iterations 1.4808961E-03 0.1936722 at 30iterations 1.4647674E-04 1.9756317E-02 at 40iterations 1.5269434E-05 1.9416809E-03 at 50iterations finished qdiffx linear iterations at : 22:10:29 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 1.5269434E-05 1.9416809E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 22:10:30 3.453u 0.180s 0:03.98 91.2% 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 Sun Oct 9 2011 at 22:10:30 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3253 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: SEP 139 has a net charge of -0.4750 !!! WARNING: GLM 422 has a net charge of -0.6000 !!! WARNING: GLM 556 has a net charge of -0.6000 !!! WARNING: ZN7 776 has a net charge of 1.4000 !!! WARNING: ZN7 780 has a net charge of 1.4000 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: 1.899038 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): 45.37700 98.40100 ymin,ymax (A): 2.955000 59.19400 zmin,zma (A): 14.90500 67.37600 x,y,z range (A): 53.02400 56.23900 52.47100 scale (grids/A): 1.899038 object centre (A): 71.88900 31.07450 41.14050 number of atom coordinates read : 3253 total number of charged atoms : 3101 net assigned charge : 6.725008 assigned positive charge : 496.5906 centred at (gu) : 91.20605 84.27046 91.45815 assigned negative charge : -489.8671 centred at (gu) : 91.00751 84.13511 91.46575 start vw surface at 0.1100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 94840 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29689 grid for indexing accessible points = 1.400000 m= 32470 mr = 64610 m= 4965 mr = 23278 m= 382 mr = 2924 m= 14 mr = 161 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 2111 time to turn everything in is 0.4700000 number of dielectric boundary points 41698 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 201 iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 24392 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) : 0.6330127 object centre at (A) : 71.88900 31.07450 41.14050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1616376E-03 -9.7300531E-03 midg,1,midg; midg,igrid,midg 8.3721891E-02 3.8800459E-02 1,midg,midg; igrid,midg,midg -2.2608902E-02 1.9845946E-02 gauss-seidel spectral radius is 0.9987002 estimated iterations to convergence 220 setup time was (sec) 0.7000000 now iterating at: 22:10:31 rms-change max change #iterations 4.816325 159.1304 at 10iterations 2.282505 73.85420 at 20iterations 1.088674 29.62266 at 30iterations 0.5189928 15.89849 at 40iterations 0.2469987 7.277036 at 50iterations 0.1177157 3.319862 at 60iterations 5.6143988E-02 1.696931 at 70iterations 2.6714630E-02 0.9827213 at 80iterations 1.2763903E-02 0.3708935 at 90iterations 6.0795792E-03 0.1736822 at 100iterations 2.8974947E-03 8.1936836E-02 at 110iterations 1.3831424E-03 4.1550636E-02 at 120iterations finished qdiffx linear iterations at : 22:10:38 total time elapsed so far: 7.970000 # loops : 120 mean,max change (kT/e) : 1.3831424E-03 4.1550636E-02 energy calculations done at 7.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.090000 DelPhi exited at 22:10:39 8.092u 0.209s 0:08.59 96.5% 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 Sun Oct 9 2011 at 22:10:39 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3253 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: SEP 139 has a net charge of -0.4750 !!! WARNING: GLM 422 has a net charge of -0.6000 !!! WARNING: GLM 556 has a net charge of -0.6000 !!! WARNING: ZN7 776 has a net charge of 1.4000 !!! WARNING: ZN7 780 has a net charge of 1.4000 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: 2.848557 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): 45.37700 98.40100 ymin,ymax (A): 2.955000 59.19400 zmin,zma (A): 14.90500 67.37600 x,y,z range (A): 53.02400 56.23900 52.47100 scale (grids/A): 2.848557 object centre (A): 71.88900 31.07450 41.14050 number of atom coordinates read : 3253 total number of charged atoms : 3101 net assigned charge : 6.725008 assigned positive charge : 496.5906 centred at (gu) : 91.80882 81.40549 92.18703 assigned negative charge : -489.8671 centred at (gu) : 91.51141 81.20230 92.19844 start vw surface at 0.1100000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 219490 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29689 grid for indexing accessible points = 1.400000 m= 106234 mr = 156984 m= 36978 mr = 85725 m= 8849 mr = 28924 m= 1471 mr = 6391 m= 125 mr = 987 m= 3 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 7254 time to turn everything in is 1.190000 number of dielectric boundary points 94079 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 24807 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) : 1.899038 object centre at (A) : 71.88900 31.07450 41.14050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2720589E-02 -0.2502956 midg,1,midg; midg,igrid,midg 0.6330410 0.4199886 1,midg,midg; igrid,midg,midg -0.2961971 0.2461280 gauss-seidel spectral radius is 0.9992950 estimated iterations to convergence 297 setup time was (sec) 1.450000 now iterating at: 22:10:40 rms-change max change #iterations 11.38454 424.8968 at 10iterations 6.790839 156.4860 at 20iterations 4.027946 90.03548 at 30iterations 2.377190 56.85901 at 40iterations 1.397425 28.66390 at 50iterations 0.8203682 15.44028 at 60iterations 0.4809930 9.274892 at 70iterations 0.2816851 5.242210 at 80iterations 0.1647779 3.083336 at 90iterations 9.6362613E-02 1.664493 at 100iterations 5.6263227E-02 0.9823025 at 110iterations 3.2789994E-02 0.6423798 at 120iterations 1.9157944E-02 0.3230371 at 130iterations 1.1167759E-02 0.2064228 at 140iterations 6.5312381E-03 0.1002426 at 150iterations 3.7999342E-03 6.3140869E-02 at 160iterations 2.2192879E-03 4.0669441E-02 at 170iterations 1.2959313E-03 2.0530701E-02 at 180iterations finished qdiffx linear iterations at : 22:10:52 total time elapsed so far: 13.34000 # loops : 180 mean,max change (kT/e) : 1.2959313E-03 2.0530701E-02 energy calculations done at 13.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.48000 DelPhi exited at 22:10:53 13.478u 0.190s 0:14.17 96.4% 0+0k 0+0io 0pf+0w