Wed Feb 15 08:57:38 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:57:38 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 ! Automatically converted by prot2crg.py # of charge parameter records: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3062 !!! WARNING: TPO 165 has a net charge of -1.7500 !!! WARNING: GLU 329 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5767330 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): -23.95000 27.49100 ymin,ymax (A): -26.24800 24.80700 zmin,zma (A): -8.739000 52.98800 x,y,z range (A): 51.44100 51.05500 61.72701 scale (grids/A): 0.5767330 object centre (A): 1.770501 -0.7205009 22.12450 number of atom coordinates read : 3062 total number of charged atoms : 2914 net assigned charge : 2.250037 assigned positive charge : 459.7828 centred at (gu) : 91.10113 89.94644 90.15296 assigned negative charge : -457.5339 centred at (gu) : 91.22202 89.92796 90.26438 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6648 nv = 96 ne = 84 npr = 62771 no. pairs analyzed = 62771 no. exposed pairs = 3894 no. arc points = 27318 no. surface atoms = 1304 nbur = 1758 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 314 mr = 3543 m= 3 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3403 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2787 ## 338 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 8617 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6107991E-09 -1.8854243E-09 midg,1,midg; midg,igrid,midg 1.0051684E-10 8.3943869E-10 1,midg,midg; igrid,midg,midg 2.2315063E-09 -2.6354541E-09 gauss-seidel spectral radius is 0.9844903 estimated iterations to convergence 66 setup time was (sec) 0.7200000 now iterating at: 08:57:39 rms-change max change #iterations 9.7107977E-02 16.29667 at 10iterations 7.7925310E-03 1.234802 at 20iterations 1.1063543E-03 0.2150650 at 30iterations 4.0998208E-04 9.1548920E-02 at 40iterations 1.7849174E-04 4.0182114E-02 at 50iterations finished qdiffx linear iterations at : 08:57:44 total time elapsed so far: 5.600000 # loops : 50 mean,max change (kT/e) : 1.7849174E-04 4.0182114E-02 energy calculations done at 5.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.780000 DelPhi exited at 08:57:45 5.788u 0.429s 0:06.54 94.8% 0+0k 0+0io 6pf+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 Wed Feb 15 2012 at 08:57:45 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 ! Automatically converted by prot2crg.py # of charge parameter records: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3062 !!! WARNING: TPO 165 has a net charge of -1.7500 !!! WARNING: GLU 329 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.730199 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): -23.95000 27.49100 ymin,ymax (A): -26.24800 24.80700 zmin,zma (A): -8.739000 52.98800 x,y,z range (A): 51.44100 51.05500 61.72701 scale (grids/A): 1.730199 object centre (A): 1.770501 -0.7205009 22.12450 number of atom coordinates read : 3062 total number of charged atoms : 2914 net assigned charge : 2.250037 assigned positive charge : 459.7828 centred at (gu) : 93.30260 89.83813 90.45805 assigned negative charge : -457.5339 centred at (gu) : 93.66559 89.78358 90.79282 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 73571 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27318 grid for indexing accessible points = 1.400000 m= 23543 mr = 50457 m= 2746 mr = 16367 m= 96 mr = 1437 m= 0 mr = 10 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 181 time to turn everything in is 0.6300000 number of dielectric boundary points 31685 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 267 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 22596 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) : 0.5767330 object centre at (A) : 1.770501 -0.7205009 22.12450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3409558E-02 2.0326864E-02 midg,1,midg; midg,igrid,midg -2.7099368E-04 1.9834167E-03 1,midg,midg; igrid,midg,midg 4.1785189E-03 -9.2048701E-03 gauss-seidel spectral radius is 0.9984025 estimated iterations to convergence 199 setup time was (sec) 1.000000 now iterating at: 08:57:46 rms-change max change #iterations 3.836083 188.5909 at 10iterations 1.680218 54.45090 at 20iterations 0.7392268 26.75928 at 30iterations 0.3255695 11.15532 at 40iterations 0.1439034 4.879271 at 50iterations 6.3225612E-02 2.056526 at 60iterations 2.7987322E-02 0.8805561 at 70iterations 1.2498440E-02 0.4244685 at 80iterations 5.7159173E-03 0.2322159 at 90iterations 2.8023520E-03 0.1045208 at 100iterations 1.5295380E-03 6.3758850E-02 at 110iterations 9.6624775E-04 4.3479919E-02 at 120iterations finished qdiffx linear iterations at : 08:57:59 total time elapsed so far: 13.38000 # loops : 120 mean,max change (kT/e) : 9.6624775E-04 4.3479919E-02 energy calculations done at 13.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.55000 DelPhi exited at 08:57:59 13.553u 0.517s 0:14.44 97.3% 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 Wed Feb 15 2012 at 08:57:59 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 ! Automatically converted by prot2crg.py # of charge parameter records: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3062 !!! WARNING: TPO 165 has a net charge of -1.7500 !!! WARNING: GLU 329 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.595299 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): -23.95000 27.49100 ymin,ymax (A): -26.24800 24.80700 zmin,zma (A): -8.739000 52.98800 x,y,z range (A): 51.44100 51.05500 61.72701 scale (grids/A): 2.595299 object centre (A): 1.770501 -0.7205009 22.12450 number of atom coordinates read : 3062 total number of charged atoms : 2914 net assigned charge : 2.250037 assigned positive charge : 459.7828 centred at (gu) : 94.95368 89.75690 90.68674 assigned negative charge : -457.5339 centred at (gu) : 95.49839 89.67529 91.18927 start vw surface at 0.1100000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 170586 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27318 grid for indexing accessible points = 1.400000 m= 80816 mr = 122992 m= 24305 mr = 64518 m= 4563 mr = 18404 m= 398 mr = 3035 m= 5 mr = 192 m= 0 mr = 3 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 619 time to turn everything in is 1.540000 number of dielectric boundary points 71529 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 23298 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) : 1.730199 object centre at (A) : 1.770501 -0.7205009 22.12450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8266115E-02 0.5391292 midg,1,midg; midg,igrid,midg -4.1796989E-03 2.6845425E-02 1,midg,midg; igrid,midg,midg 1.9634053E-02 -0.1054485 gauss-seidel spectral radius is 0.9992072 estimated iterations to convergence 280 setup time was (sec) 1.940000 now iterating at: 08:58:02 rms-change max change #iterations 9.539946 323.1357 at 10iterations 5.485115 131.6652 at 20iterations 3.154346 65.12602 at 30iterations 1.797050 39.85474 at 40iterations 1.023569 21.41542 at 50iterations 0.5804417 12.06250 at 60iterations 0.3295873 6.376837 at 70iterations 0.1864851 3.770005 at 80iterations 0.1057937 2.055013 at 90iterations 5.9683762E-02 1.174091 at 100iterations 3.3849381E-02 0.6540900 at 110iterations 1.9187273E-02 0.3772182 at 120iterations 1.0919162E-02 0.2249393 at 130iterations 6.3012359E-03 0.1333847 at 140iterations 3.7166274E-03 8.0112457E-02 at 150iterations 2.2925315E-03 5.8307648E-02 at 160iterations 1.5085739E-03 3.5774708E-02 at 170iterations 1.0738700E-03 2.7478218E-02 at 180iterations finished qdiffx linear iterations at : 08:58:22 total time elapsed so far: 22.15000 # loops : 180 mean,max change (kT/e) : 1.0738700E-03 2.7478218E-02 energy calculations done at 22.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.31000 DelPhi exited at 08:58:22 22.315u 0.579s 0:23.19 98.6% 0+0k 0+0io 0pf+0w