Tue Oct 11 06:00:05 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 Tue Oct 11 2011 at 06:00:05 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 = 2049 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: 0.7607813 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): -18.03200 28.76200 ymin,ymax (A): -11.74300 30.70500 zmin,zma (A): -8.506000 38.07600 x,y,z range (A): 46.79400 42.44800 46.58200 scale (grids/A): 0.7607813 object centre (A): 5.365000 9.481000 14.78500 number of atom coordinates read : 2049 total number of charged atoms : 1921 net assigned charge : 7.500009 assigned positive charge : 310.2271 centred at (gu) : 90.44615 89.84869 90.91721 assigned negative charge : -302.7272 centred at (gu) : 90.31781 89.77600 90.78593 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8265 nv = 96 ne = 84 npr = 41092 no. pairs analyzed = 41092 no. exposed pairs = 2512 no. arc points = 17143 no. surface atoms = 852 nbur = 1197 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 619 mr = 4911 m= 5 mr = 136 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.2600000 number of dielectric boundary points 3842 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1434 ## 114 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 8523 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.9352109E-09 4.6153107E-07 midg,1,midg; midg,igrid,midg 9.8558587E-08 2.9890219E-07 1,midg,midg; igrid,midg,midg 1.3795689E-08 4.1895660E-07 gauss-seidel spectral radius is 0.9909808 estimated iterations to convergence 85 setup time was (sec) 0.4800000 now iterating at: 06:00:06 rms-change max change #iterations 0.2649603 41.72806 at 10iterations 3.8230978E-02 4.974542 at 20iterations 5.6201462E-03 0.6754436 at 30iterations 8.8677910E-04 0.1040773 at 40iterations 1.9473484E-04 2.5884628E-02 at 50iterations finished qdiffx linear iterations at : 06:00:08 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.9473484E-04 2.5884628E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 06:00:09 3.370u 0.175s 0:04.16 85.0% 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 06:00:09 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 = 2049 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: 2.282344 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): -18.03200 28.76200 ymin,ymax (A): -11.74300 30.70500 zmin,zma (A): -8.506000 38.07600 x,y,z range (A): 46.79400 42.44800 46.58200 scale (grids/A): 2.282344 object centre (A): 5.365000 9.481000 14.78500 number of atom coordinates read : 2049 total number of charged atoms : 1921 net assigned charge : 7.500009 assigned positive charge : 310.2271 centred at (gu) : 91.33834 89.54599 92.75159 assigned negative charge : -302.7272 centred at (gu) : 90.95343 89.32817 92.35786 start vw surface at 0.1300000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 86263 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17143 grid for indexing accessible points = 1.400000 m= 37938 mr = 62050 m= 8621 mr = 29620 m= 1036 mr = 6115 m= 51 mr = 604 m= 0 mr = 9 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 197 time to turn everything in is 0.6900000 number of dielectric boundary points 35511 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 39 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 15320 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) : 0.7607813 object centre at (A) : 5.365000 9.481000 14.78500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.6464620E-02 5.6216836E-02 midg,1,midg; midg,igrid,midg 3.7791226E-02 3.5552986E-02 1,midg,midg; igrid,midg,midg 5.3664275E-02 0.1241341 gauss-seidel spectral radius is 0.9989629 estimated iterations to convergence 246 setup time was (sec) 0.9500000 now iterating at: 06:00:10 rms-change max change #iterations 5.166158 220.2441 at 10iterations 2.681870 89.15200 at 20iterations 1.379037 48.61280 at 30iterations 0.7156110 19.32587 at 40iterations 0.3692240 10.12546 at 50iterations 0.1908122 6.005791 at 60iterations 9.8943807E-02 2.778250 at 70iterations 5.1128928E-02 1.419785 at 80iterations 2.6589176E-02 0.7004604 at 90iterations 1.3796070E-02 0.3839417 at 100iterations 7.2199209E-03 0.2015648 at 110iterations 3.7908833E-03 0.1052856 at 120iterations finished qdiffx linear iterations at : 06:00:17 total time elapsed so far: 7.370000 # loops : 120 mean,max change (kT/e) : 3.7908833E-03 0.1052856 energy calculations done at 7.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.540000 DelPhi exited at 06:00:17 7.543u 0.210s 0:08.14 95.2% 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 Tue Oct 11 2011 at 06:00:17 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 = 2049 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.423516 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): -18.03200 28.76200 ymin,ymax (A): -11.74300 30.70500 zmin,zma (A): -8.506000 38.07600 x,y,z range (A): 46.79400 42.44800 46.58200 scale (grids/A): 3.423516 object centre (A): 5.365000 9.481000 14.78500 number of atom coordinates read : 2049 total number of charged atoms : 1921 net assigned charge : 7.500009 assigned positive charge : 310.2271 centred at (gu) : 92.00761 89.31909 94.12740 assigned negative charge : -302.7272 centred at (gu) : 91.43011 88.99227 93.53679 start vw surface at 0.1200000 fill in re-entrant regions at 0.8800000 boundary points on vw surface= 198197 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17143 grid for indexing accessible points = 1.400000 m= 113957 mr = 148479 m= 51644 mr = 96253 m= 17006 mr = 43565 m= 4099 mr = 13659 m= 673 mr = 3185 m= 52 mr = 466 m= 5 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 720 time to turn everything in is 2.120000 number of dielectric boundary points 80000 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.260000 number of grid points assigned charge 15368 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) : 2.282344 object centre at (A) : 5.365000 9.481000 14.78500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6203616 0.4842502 midg,1,midg; midg,igrid,midg 0.3011255 0.1474694 1,midg,midg; igrid,midg,midg 0.3231400 0.8337911 gauss-seidel spectral radius is 0.9993310 estimated iterations to convergence 305 setup time was (sec) 2.430000 now iterating at: 06:00:20 rms-change max change #iterations 11.14915 393.6412 at 10iterations 6.736801 151.0328 at 20iterations 4.044232 76.51866 at 30iterations 2.417831 40.18462 at 40iterations 1.444550 27.87328 at 50iterations 0.8655682 15.97091 at 60iterations 0.5145428 8.942673 at 70iterations 0.3063892 5.628482 at 80iterations 0.1823653 3.328163 at 90iterations 0.1084679 1.713151 at 100iterations 6.4498276E-02 1.102378 at 110iterations 3.8549174E-02 0.6632247 at 120iterations 2.3050636E-02 0.3891888 at 130iterations 1.3947738E-02 0.2607670 at 140iterations 8.6024227E-03 0.1421328 at 150iterations 5.4617096E-03 9.3452454E-02 at 160iterations 3.6322151E-03 6.3972473E-02 at 170iterations 2.5613145E-03 4.4212341E-02 at 180iterations finished qdiffx linear iterations at : 06:00:31 total time elapsed so far: 13.67000 # loops : 180 mean,max change (kT/e) : 2.5613145E-03 4.4212341E-02 energy calculations done at 13.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.83000 DelPhi exited at 06:00:32 13.836u 0.262s 0:14.41 97.7% 0+0k 0+0io 0pf+0w