Sat Oct 15 13:13:31 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 13:13:32 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3319 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 0.5721816 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): -11.18200 51.03600 ymin,ymax (A): -12.90100 42.54800 zmin,zma (A): 19.68200 75.90100 x,y,z range (A): 62.21800 55.44900 56.21900 scale (grids/A): 0.5721816 object centre (A): 19.92700 14.82350 47.79150 number of atom coordinates read : 3319 total number of charged atoms : 3163 net assigned charge : 4.240020 assigned positive charge : 512.0815 centred at (gu) : 90.89579 89.84836 87.87840 assigned negative charge : -507.8430 centred at (gu) : 90.77520 89.94407 87.84989 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7324 nv = 96 ne = 84 npr = 63907 no. pairs analyzed = 63907 no. exposed pairs = 4524 no. arc points = 31837 no. surface atoms = 1516 nbur = 1803 mkacc time = 9.9999994E-02 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 = 1.484000 m= 382 mr = 3657 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 4025 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3101 ## 321 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9153 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0245898E-10 7.5481726E-10 midg,1,midg; midg,igrid,midg 2.5989861E-09 -1.1298740E-09 1,midg,midg; igrid,midg,midg -1.3359865E-09 3.6849837E-09 gauss-seidel spectral radius is 0.9842737 estimated iterations to convergence 66 setup time was (sec) 0.4200000 now iterating at: 13:13:32 rms-change max change #iterations 9.6184410E-02 15.52263 at 10iterations 7.2467537E-03 1.083400 at 20iterations 5.5325677E-04 9.5494270E-02 at 30iterations 4.1173938E-05 5.9967041E-03 at 40iterations 3.3087372E-06 4.1580200E-04 at 50iterations finished qdiffx linear iterations at : 13:13:35 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 3.3087372E-06 4.1580200E-04 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 13:13:36 3.523u 0.201s 0:04.35 85.5% 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 Sat Oct 15 2011 at 13:13:36 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3319 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 1.716545 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): -11.18200 51.03600 ymin,ymax (A): -12.90100 42.54800 zmin,zma (A): 19.68200 75.90100 x,y,z range (A): 62.21800 55.44900 56.21900 scale (grids/A): 1.716545 object centre (A): 19.92700 14.82350 47.79150 number of atom coordinates read : 3319 total number of charged atoms : 3163 net assigned charge : 4.240020 assigned positive charge : 512.0815 centred at (gu) : 92.68662 89.54432 83.63451 assigned negative charge : -507.8430 centred at (gu) : 92.32530 89.83199 83.54944 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 80093 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31837 grid for indexing accessible points = 1.400000 m= 26996 mr = 53424 m= 3524 mr = 18248 m= 158 mr = 1801 m= 1 mr = 30 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 0.4000000 number of dielectric boundary points 37269 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 297 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 24474 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) : 0.5721816 object centre at (A) : 19.92700 14.82350 47.79150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4404695E-02 6.3086138E-03 midg,1,midg; midg,igrid,midg 2.0407900E-02 -8.5196486E-03 1,midg,midg; igrid,midg,midg -5.9526367E-03 1.9232627E-02 gauss-seidel spectral radius is 0.9984068 estimated iterations to convergence 199 setup time was (sec) 0.6300000 now iterating at: 13:13:37 rms-change max change #iterations 4.056178 169.1833 at 10iterations 1.782241 61.45184 at 20iterations 0.7892563 26.40722 at 30iterations 0.3479717 11.67533 at 40iterations 0.1543045 4.671783 at 50iterations 6.7934997E-02 2.583504 at 60iterations 3.0123191E-02 1.213072 at 70iterations 1.3302383E-02 0.4173965 at 80iterations 5.8869822E-03 0.2202883 at 90iterations 2.6026946E-03 9.5840454E-02 at 100iterations 1.1632871E-03 4.1374207E-02 at 110iterations 5.3276116E-04 1.8157959E-02 at 120iterations finished qdiffx linear iterations at : 13:13:44 total time elapsed so far: 8.150000 # loops : 120 mean,max change (kT/e) : 5.3276116E-04 1.8157959E-02 energy calculations done at 8.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.290000 DelPhi exited at 13:13:45 8.290u 0.228s 0:09.01 94.4% 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 13:13:45 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 # of charge parameter records: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3319 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 2.574817 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): -11.18200 51.03600 ymin,ymax (A): -12.90100 42.54800 zmin,zma (A): 19.68200 75.90100 x,y,z range (A): 62.21800 55.44900 56.21900 scale (grids/A): 2.574817 object centre (A): 19.92700 14.82350 47.79150 number of atom coordinates read : 3319 total number of charged atoms : 3163 net assigned charge : 4.240020 assigned positive charge : 512.0815 centred at (gu) : 94.02963 89.31615 80.45129 assigned negative charge : -507.8430 centred at (gu) : 93.48782 89.74788 80.32404 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 185669 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31837 grid for indexing accessible points = 1.400000 m= 89747 mr = 130988 m= 29221 mr = 70180 m= 5771 mr = 21651 m= 617 mr = 3851 m= 19 mr = 350 m= 0 mr = 2 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.010000 number of dielectric boundary points 84022 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 25258 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) : 1.716545 object centre at (A) : 19.92700 14.82350 47.79150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2879469 7.7209018E-02 midg,1,midg; midg,igrid,midg 0.2682280 -0.1099548 1,midg,midg; igrid,midg,midg 0.1416244 0.2291512 gauss-seidel spectral radius is 0.9992220 estimated iterations to convergence 283 setup time was (sec) 1.280000 now iterating at: 13:13:46 rms-change max change #iterations 10.39739 415.1005 at 10iterations 6.158281 208.5212 at 20iterations 3.597214 88.38244 at 30iterations 2.081956 50.58595 at 40iterations 1.203331 29.97835 at 50iterations 0.6902316 17.11907 at 60iterations 0.3958031 9.605745 at 70iterations 0.2265944 5.555294 at 80iterations 0.1293796 2.672462 at 90iterations 7.3819011E-02 1.509170 at 100iterations 4.2089168E-02 0.8529482 at 110iterations 2.4003690E-02 0.4878697 at 120iterations 1.3662096E-02 0.2854414 at 130iterations 7.8021963E-03 0.1764893 at 140iterations 4.4671306E-03 9.7167730E-02 at 150iterations 2.5860984E-03 5.3277969E-02 at 160iterations 1.5349142E-03 3.1127930E-02 at 170iterations 9.5551560E-04 2.0166516E-02 at 180iterations finished qdiffx linear iterations at : 13:13:59 total time elapsed so far: 13.42000 # loops : 180 mean,max change (kT/e) : 9.5551560E-04 2.0166516E-02 energy calculations done at 13.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.55000 DelPhi exited at 13:13:59 13.549u 0.243s 0:14.10 97.7% 0+0k 0+0io 0pf+0w