Mon Oct 10 14:15:54 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 Mon Oct 10 2011 at 14:15:54 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3986 !!! WARNING: ADP 663 has a net charge of -2.0000 !!! WARNING: MG6 664 has a net charge of 1.4000 !!! WARNING: MG6 665 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.4924677 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): -1.844000 51.19100 ymin,ymax (A): -16.42400 46.69800 zmin,zma (A): -20.74000 51.54900 x,y,z range (A): 53.03500 63.12200 72.28900 scale (grids/A): 0.4924677 object centre (A): 24.67350 15.13700 15.40450 number of atom coordinates read : 3986 total number of charged atoms : 3802 net assigned charge : -5.699986 assigned positive charge : 625.7184 centred at (gu) : 89.24905 89.85332 89.19825 assigned negative charge : -631.4216 centred at (gu) : 89.29018 89.87012 89.29198 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6283 nv = 96 ne = 84 npr = 75197 no. pairs analyzed = 75197 no. exposed pairs = 6029 no. arc points = 41384 no. surface atoms = 1984 nbur = 2002 mkacc time = 0.1400000 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 = 1.736000 m= 252 mr = 2776 m= 0 mr = 6 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3753 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3898 ## 626 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 8363 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.3897451E-11 -1.0741909E-10 midg,1,midg; midg,igrid,midg -1.9678573E-11 -5.1389441E-11 1,midg,midg; igrid,midg,midg 7.5516433E-12 -6.4187183E-11 gauss-seidel spectral radius is 0.9788824 estimated iterations to convergence 57 setup time was (sec) 0.4600000 now iterating at: 14:15:55 rms-change max change #iterations 5.2407771E-02 9.481247 at 10iterations 3.0720071E-03 0.5264435 at 20iterations 4.9049023E-04 6.6329956E-02 at 30iterations 1.6239219E-04 2.2928238E-02 at 40iterations 5.9076523E-05 8.1901550E-03 at 50iterations finished qdiffx linear iterations at : 14:15:59 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 5.9076523E-05 8.1901550E-03 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 14:16:01 3.529u 0.330s 0:06.07 63.4% 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 Mon Oct 10 2011 at 14:16:01 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3986 !!! WARNING: ADP 663 has a net charge of -2.0000 !!! WARNING: MG6 664 has a net charge of 1.4000 !!! WARNING: MG6 665 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.477403 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): -1.844000 51.19100 ymin,ymax (A): -16.42400 46.69800 zmin,zma (A): -20.74000 51.54900 x,y,z range (A): 53.03500 63.12200 72.28900 scale (grids/A): 1.477403 object centre (A): 24.67350 15.13700 15.40450 number of atom coordinates read : 3986 total number of charged atoms : 3802 net assigned charge : -5.699986 assigned positive charge : 625.7184 centred at (gu) : 87.74630 89.55904 87.59333 assigned negative charge : -631.4216 centred at (gu) : 87.87012 89.60989 87.87543 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 70549 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41384 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 18690 mr = 44401 m= 1406 mr = 10622 m= 29 mr = 422 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 35229 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 584 ## 11 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 28168 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) : 0.4924677 object centre at (A) : 24.67350 15.13700 15.40450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0448600E-02 -3.8837607E-03 midg,1,midg; midg,igrid,midg 9.7344245E-04 4.8675062E-03 1,midg,midg; igrid,midg,midg -2.0313682E-03 -9.6342936E-03 gauss-seidel spectral radius is 0.9978985 estimated iterations to convergence 174 setup time was (sec) 0.5900000 now iterating at: 14:16:02 rms-change max change #iterations 3.239073 149.9866 at 10iterations 1.256241 56.18439 at 20iterations 0.4850263 19.17055 at 30iterations 0.1897238 7.150889 at 40iterations 7.3510654E-02 2.671203 at 50iterations 2.8693380E-02 1.161015 at 60iterations 1.1260098E-02 0.4149399 at 70iterations 4.4572824E-03 0.1757488 at 80iterations 1.8228088E-03 7.2158813E-02 at 90iterations 8.0020865E-04 2.9968262E-02 at 100iterations 4.0144552E-04 1.5817165E-02 at 110iterations 2.3341147E-04 7.6904297E-03 at 120iterations finished qdiffx linear iterations at : 14:16:12 total time elapsed so far: 7.700000 # loops : 120 mean,max change (kT/e) : 2.3341147E-04 7.6904297E-03 energy calculations done at 7.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 14:16:12 7.823u 0.606s 0:11.75 71.6% 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 14:16:12 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3986 !!! WARNING: ADP 663 has a net charge of -2.0000 !!! WARNING: MG6 664 has a net charge of 1.4000 !!! WARNING: MG6 665 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.216105 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): -1.844000 51.19100 ymin,ymax (A): -16.42400 46.69800 zmin,zma (A): -20.74000 51.54900 x,y,z range (A): 53.03500 63.12200 72.28900 scale (grids/A): 2.216105 object centre (A): 24.67350 15.13700 15.40450 number of atom coordinates read : 3986 total number of charged atoms : 3802 net assigned charge : -5.699986 assigned positive charge : 625.7184 centred at (gu) : 86.61908 89.33811 86.38978 assigned negative charge : -631.4216 centred at (gu) : 86.80515 89.41483 86.81303 start vw surface at 0.1100000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 164199 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41384 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 67823 mr = 110861 m= 15462 mr = 48376 m= 1802 mr = 9644 m= 53 mr = 805 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8500000 number of dielectric boundary points 79650 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 94 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 30283 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) : 1.477403 object centre at (A) : 24.67350 15.13700 15.40450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2749439 0.1471711 midg,1,midg; midg,igrid,midg 4.1427989E-02 0.1130721 1,midg,midg; igrid,midg,midg -1.6441617E-02 -0.1764840 gauss-seidel spectral radius is 0.9990934 estimated iterations to convergence 262 setup time was (sec) 1.090000 now iterating at: 14:16:14 rms-change max change #iterations 9.348547 331.3796 at 10iterations 5.319160 155.5289 at 20iterations 3.007844 89.33017 at 30iterations 1.683972 41.94191 at 40iterations 0.9366221 25.19604 at 50iterations 0.5173892 12.80013 at 60iterations 0.2854191 7.800117 at 70iterations 0.1566745 4.505058 at 80iterations 8.5815869E-02 1.885543 at 90iterations 4.7034439E-02 1.126261 at 100iterations 2.5722669E-02 0.6139145 at 110iterations 1.4039596E-02 0.3494110 at 120iterations 7.6561258E-03 0.1787510 at 130iterations 4.1688546E-03 9.7941875E-02 at 140iterations 2.2854994E-03 5.1286697E-02 at 150iterations 1.2513933E-03 2.8509617E-02 at 160iterations 6.9367146E-04 1.6460419E-02 at 170iterations 3.9156814E-04 9.5081329E-03 at 180iterations finished qdiffx linear iterations at : 14:16:28 total time elapsed so far: 12.51000 # loops : 180 mean,max change (kT/e) : 3.9156814E-04 9.5081329E-03 energy calculations done at 12.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.63000 DelPhi exited at 14:16:29 12.636u 0.629s 0:16.47 80.4% 0+0k 0+0io 0pf+0w