Tue Oct 11 03:19:27 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 03:19:27 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 = 4675 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.4963886 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): -4.362000 57.66600 ymin,ymax (A): -46.72200 21.17800 zmin,zma (A): -56.22800 15.49000 x,y,z range (A): 62.02800 67.90000 71.71800 scale (grids/A): 0.4963886 object centre (A): 26.65200 -12.77200 -20.36900 number of atom coordinates read : 4675 total number of charged atoms : 4526 net assigned charge : -5.499936 assigned positive charge : 695.9225 centred at (gu) : 90.62410 90.53472 91.63999 assigned negative charge : -701.4269 centred at (gu) : 90.59077 90.57226 91.63435 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7465 nv = 96 ne = 84 npr = 91802 no. pairs analyzed = 91802 no. exposed pairs = 6383 no. arc points = 44251 no. surface atoms = 2118 nbur = 2557 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 = 1.736000 m= 221 mr = 3586 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 4098 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4269 ## 673 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 9996 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.1448757E-11 -5.0798803E-11 midg,1,midg; midg,igrid,midg 8.4690735E-12 -1.0623927E-10 1,midg,midg; igrid,midg,midg -7.2883012E-11 5.5645471E-12 gauss-seidel spectral radius is 0.9792596 estimated iterations to convergence 57 setup time was (sec) 0.5000000 now iterating at: 03:19:28 rms-change max change #iterations 5.4502230E-02 8.451497 at 10iterations 2.9909543E-03 0.4027281 at 20iterations 3.4206157E-04 4.6558380E-02 at 30iterations 1.0994787E-04 1.3094902E-02 at 40iterations 3.9068738E-05 4.5185089E-03 at 50iterations finished qdiffx linear iterations at : 03:19:31 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 3.9068738E-05 4.5185089E-03 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 03:19:31 3.586u 0.193s 0:04.30 87.6% 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 Tue Oct 11 2011 at 03:19:31 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 = 4675 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.489166 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): -4.362000 57.66600 ymin,ymax (A): -46.72200 21.17800 zmin,zma (A): -56.22800 15.49000 x,y,z range (A): 62.02800 67.90000 71.71800 scale (grids/A): 1.489166 object centre (A): 26.65200 -12.77200 -20.36900 number of atom coordinates read : 4675 total number of charged atoms : 4526 net assigned charge : -5.499936 assigned positive charge : 695.9225 centred at (gu) : 91.87101 91.60268 94.91861 assigned negative charge : -701.4269 centred at (gu) : 91.77190 91.71642 94.90275 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 84113 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44251 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 23146 mr = 55405 m= 1772 mr = 14637 m= 35 mr = 613 m= 2 mr = 1 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 0.4200000 number of dielectric boundary points 38412 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 669 ## 13 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 33658 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) : 0.4963886 object centre at (A) : 26.65200 -12.77200 -20.36900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.1648858E-03 7.4802837E-03 midg,1,midg; midg,igrid,midg -5.8047739E-03 -1.0387078E-02 1,midg,midg; igrid,midg,midg -9.2337495E-03 4.4986946E-03 gauss-seidel spectral radius is 0.9979979 estimated iterations to convergence 178 setup time was (sec) 0.6400000 now iterating at: 03:19:32 rms-change max change #iterations 3.482974 150.5582 at 10iterations 1.389939 56.43882 at 20iterations 0.5544721 20.03407 at 30iterations 0.2204518 7.883668 at 40iterations 8.8342160E-02 2.788044 at 50iterations 3.5172798E-02 1.277934 at 60iterations 1.4121027E-02 0.4939880 at 70iterations 5.6526307E-03 0.1823044 at 80iterations 2.2893641E-03 7.6057434E-02 at 90iterations 9.4456825E-04 3.1099319E-02 at 100iterations 4.1046413E-04 1.3015747E-02 at 110iterations 1.9544267E-04 6.3524246E-03 at 120iterations finished qdiffx linear iterations at : 03:19:39 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 1.9544267E-04 6.3524246E-03 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 03:19:40 7.873u 0.214s 0:08.46 95.5% 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 Tue Oct 11 2011 at 03:19:40 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 = 4675 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.233749 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): -4.362000 57.66600 ymin,ymax (A): -46.72200 21.17800 zmin,zma (A): -56.22800 15.49000 x,y,z range (A): 62.02800 67.90000 71.71800 scale (grids/A): 2.233749 object centre (A): 26.65200 -12.77200 -20.36900 number of atom coordinates read : 4675 total number of charged atoms : 4526 net assigned charge : -5.499936 assigned positive charge : 695.9225 centred at (gu) : 92.80617 92.40378 97.37762 assigned negative charge : -701.4269 centred at (gu) : 92.65781 92.57449 97.35401 start vw surface at 0.1300000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 195517 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44251 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 84218 mr = 136717 m= 19684 mr = 63757 m= 2373 mr = 13502 m= 124 mr = 1192 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.020000 number of dielectric boundary points 86729 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 109 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 36064 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) : 1.489166 object centre at (A) : 26.65200 -12.77200 -20.36900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1387873 0.3578952 midg,1,midg; midg,igrid,midg -7.9315372E-02 -0.1627964 1,midg,midg; igrid,midg,midg -0.2075457 9.4883479E-02 gauss-seidel spectral radius is 0.9991418 estimated iterations to convergence 270 setup time was (sec) 1.270000 now iterating at: 03:19:41 rms-change max change #iterations 9.913254 286.4804 at 10iterations 5.699635 145.3965 at 20iterations 3.259187 73.56110 at 30iterations 1.849729 49.31184 at 40iterations 1.041758 24.72651 at 50iterations 0.5858588 13.46420 at 60iterations 0.3281679 7.635335 at 70iterations 0.1830868 4.000299 at 80iterations 0.1021567 2.181302 at 90iterations 5.6787275E-02 1.246883 at 100iterations 3.1455595E-02 0.6605527 at 110iterations 1.7477006E-02 0.3492126 at 120iterations 9.7068679E-03 0.1910620 at 130iterations 5.3784703E-03 0.1104393 at 140iterations 2.9775670E-03 6.2519073E-02 at 150iterations 1.6490935E-03 3.4864426E-02 at 160iterations 9.1002230E-04 1.8908501E-02 at 170iterations 5.0514739E-04 1.0039330E-02 at 180iterations finished qdiffx linear iterations at : 03:19:53 total time elapsed so far: 12.96000 # loops : 180 mean,max change (kT/e) : 5.0514739E-04 1.0039330E-02 energy calculations done at 12.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.10000 DelPhi exited at 03:19:54 13.100u 0.218s 0:13.91 95.6% 0+0k 0+0io 0pf+0w