Mon Oct 10 14:00:01 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 Mon Oct 10 2011 at 14:00:01 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 = 2550 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6472256 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): 6.400000 58.99500 ymin,ymax (A): 22.00100 77.00500 zmin,zma (A): -8.432000 40.48700 x,y,z range (A): 52.59500 55.00401 48.91900 scale (grids/A): 0.6472256 object centre (A): 32.69750 49.50300 16.02750 number of atom coordinates read : 2550 total number of charged atoms : 2413 net assigned charge : 6.500017 assigned positive charge : 382.0989 centred at (gu) : 92.71476 89.53979 88.15936 assigned negative charge : -375.5995 centred at (gu) : 92.66010 89.50695 88.18305 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7299 nv = 96 ne = 84 npr = 50914 no. pairs analyzed = 50914 no. exposed pairs = 3298 no. arc points = 23320 no. surface atoms = 1105 nbur = 1445 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 391 mr = 3880 m= 3 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3774 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2254 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8602 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1174369E-08 5.5629439E-09 midg,1,midg; midg,igrid,midg 7.3858866E-09 1.4225878E-08 1,midg,midg; igrid,midg,midg 2.3179576E-09 3.3051712E-08 gauss-seidel spectral radius is 0.9876294 estimated iterations to convergence 73 setup time was (sec) 0.4100000 now iterating at: 14:00:01 rms-change max change #iterations 0.1483824 21.55059 at 10iterations 1.5400188E-02 2.284381 at 20iterations 1.5982754E-03 0.2195873 at 30iterations 2.0629953E-04 3.5427094E-02 at 40iterations 4.9724822E-05 7.0338249E-03 at 50iterations finished qdiffx linear iterations at : 14:00:05 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 4.9724822E-05 7.0338249E-03 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 14:00:05 3.578u 0.192s 0:04.41 85.2% 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 Mon Oct 10 2011 at 14:00:05 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 = 2550 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.941677 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): 6.400000 58.99500 ymin,ymax (A): 22.00100 77.00500 zmin,zma (A): -8.432000 40.48700 x,y,z range (A): 52.59500 55.00401 48.91900 scale (grids/A): 1.941677 object centre (A): 32.69750 49.50300 16.02750 number of atom coordinates read : 2550 total number of charged atoms : 2413 net assigned charge : 6.500017 assigned positive charge : 382.0989 centred at (gu) : 98.14375 88.61887 84.47772 assigned negative charge : -375.5995 centred at (gu) : 97.98022 88.52068 84.54884 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 78535 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23320 grid for indexing accessible points = 1.400000 m= 28418 mr = 53908 m= 4578 mr = 20290 m= 322 mr = 2711 m= 6 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 34849 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 18995 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) : 0.6472256 object centre at (A) : 32.69750 49.50300 16.02750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7559911E-03 -1.2462441E-02 midg,1,midg; midg,igrid,midg -2.5722036E-02 4.0381581E-02 1,midg,midg; igrid,midg,midg 2.8907988E-02 3.9893609E-02 gauss-seidel spectral radius is 0.9986815 estimated iterations to convergence 218 setup time was (sec) 0.6100000 now iterating at: 14:00:06 rms-change max change #iterations 4.347229 171.5100 at 10iterations 2.055801 68.10059 at 20iterations 0.9776251 31.71373 at 30iterations 0.4643423 14.91702 at 40iterations 0.2206594 7.317880 at 50iterations 0.1047345 3.411796 at 60iterations 4.9795780E-02 1.702664 at 70iterations 2.3689451E-02 0.7828035 at 80iterations 1.1196795E-02 0.4076653 at 90iterations 5.3189183E-03 0.1522865 at 100iterations 2.5236204E-03 9.0572357E-02 at 110iterations 1.2041705E-03 3.5915136E-02 at 120iterations finished qdiffx linear iterations at : 14:00:14 total time elapsed so far: 7.950000 # loops : 120 mean,max change (kT/e) : 1.2041705E-03 3.5915136E-02 energy calculations done at 7.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.080000 DelPhi exited at 14:00:14 8.086u 0.226s 0:08.65 95.9% 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 Mon Oct 10 2011 at 14:00:14 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 = 2550 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: 2.912515 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): 6.400000 58.99500 ymin,ymax (A): 22.00100 77.00500 zmin,zma (A): -8.432000 40.48700 x,y,z range (A): 52.59500 55.00401 48.91900 scale (grids/A): 2.912515 object centre (A): 32.69750 49.50300 16.02750 number of atom coordinates read : 2550 total number of charged atoms : 2413 net assigned charge : 6.500017 assigned positive charge : 382.0989 centred at (gu) : 102.2156 87.92804 81.71642 assigned negative charge : -375.5995 centred at (gu) : 101.9702 87.78094 81.82329 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 181175 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23320 grid for indexing accessible points = 1.400000 m= 91657 mr = 130667 m= 33364 mr = 74002 m= 8246 mr = 25917 m= 1261 mr = 5891 m= 78 mr = 800 m= 0 mr = 21 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.010000 number of dielectric boundary points 78483 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 19304 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) : 1.941677 object centre at (A) : 32.69750 49.50300 16.02750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.6082816E-02 -0.1796055 midg,1,midg; midg,igrid,midg -0.8947619 0.3944387 1,midg,midg; igrid,midg,midg 0.2939599 0.3406637 gauss-seidel spectral radius is 0.9992818 estimated iterations to convergence 294 setup time was (sec) 1.250000 now iterating at: 14:00:15 rms-change max change #iterations 10.26521 314.0469 at 10iterations 6.107371 139.1426 at 20iterations 3.627196 90.33935 at 30iterations 2.137629 46.39909 at 40iterations 1.256155 26.28842 at 50iterations 0.7362111 15.56293 at 60iterations 0.4300587 8.171592 at 70iterations 0.2503602 4.587568 at 80iterations 0.1460167 3.076492 at 90iterations 8.5240968E-02 1.675857 at 100iterations 4.9533483E-02 0.9480371 at 110iterations 2.8843118E-02 0.5285683 at 120iterations 1.6755372E-02 0.3059263 at 130iterations 9.7463438E-03 0.2047625 at 140iterations 5.6600878E-03 0.1109195 at 150iterations 3.2941578E-03 6.4680099E-02 at 160iterations 1.9174617E-03 3.2760620E-02 at 170iterations 1.1189125E-03 2.0648241E-02 at 180iterations finished qdiffx linear iterations at : 14:00:27 total time elapsed so far: 13.11000 # loops : 180 mean,max change (kT/e) : 1.1189125E-03 2.0648241E-02 energy calculations done at 13.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.25000 DelPhi exited at 14:00:29 13.250u 0.268s 0:14.88 90.7% 0+0k 0+0io 0pf+0w