Sun Oct 9 23:07:24 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 Sun Oct 9 2011 at 23:07:24 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3470 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: 0.5366214 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): -46.77900 10.56700 ymin,ymax (A): -20.76100 45.58000 zmin,zma (A): -93.80200 -32.92700 x,y,z range (A): 57.34600 66.34100 60.87500 scale (grids/A): 0.5366214 object centre (A): -18.10600 12.40950 -63.36450 number of atom coordinates read : 3470 total number of charged atoms : 3321 net assigned charge : 8.500010 assigned positive charge : 531.1578 centred at (gu) : 90.89642 88.83131 90.01092 assigned negative charge : -522.6595 centred at (gu) : 91.07532 88.83327 90.05434 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6551 nv = 96 ne = 84 npr = 66358 no. pairs analyzed = 66358 no. exposed pairs = 4954 no. arc points = 36571 no. surface atoms = 1641 nbur = 1829 mkacc time = 0.1200000 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 = 1.596000 m= 228 mr = 2865 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3909 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3734 ## 578 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 8716 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.0862920E-10 1.3653041E-10 midg,1,midg; midg,igrid,midg 5.1377963E-10 2.7410035E-10 1,midg,midg; igrid,midg,midg 1.0612115E-09 -7.9179435E-10 gauss-seidel spectral radius is 0.9821598 estimated iterations to convergence 62 setup time was (sec) 0.4500000 now iterating at: 23:07:25 rms-change max change #iterations 7.3381178E-02 12.14005 at 10iterations 4.5655174E-03 0.7565393 at 20iterations 3.1890097E-04 4.8544049E-02 at 30iterations 4.3924971E-05 5.8746338E-03 at 40iterations 1.1613022E-05 1.3725758E-03 at 50iterations finished qdiffx linear iterations at : 23:07:28 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 1.1613022E-05 1.3725758E-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 23:07:28 3.573u 0.481s 0:04.33 93.5% 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 Sun Oct 9 2011 at 23:07:28 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3470 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: 1.609864 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): -46.77900 10.56700 ymin,ymax (A): -20.76100 45.58000 zmin,zma (A): -93.80200 -32.92700 x,y,z range (A): 57.34600 66.34100 60.87500 scale (grids/A): 1.609864 object centre (A): -18.10600 12.40950 -63.36450 number of atom coordinates read : 3470 total number of charged atoms : 3321 net assigned charge : 8.500010 assigned positive charge : 531.1578 centred at (gu) : 92.68835 86.49305 90.03149 assigned negative charge : -522.6595 centred at (gu) : 93.22547 86.49938 90.16241 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 71555 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36571 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 20426 mr = 43794 m= 2087 mr = 12851 m= 63 mr = 855 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 138 time to turn everything in is 0.3600000 number of dielectric boundary points 36629 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 483 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 25265 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) : 0.5366214 object centre at (A) : -18.10600 12.40950 -63.36450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3877025E-02 5.5327541E-03 midg,1,midg; midg,igrid,midg 2.7332274E-02 2.5426708E-03 1,midg,midg; igrid,midg,midg 6.6142306E-03 -1.6347034E-02 gauss-seidel spectral radius is 0.9982150 estimated iterations to convergence 188 setup time was (sec) 0.5800000 now iterating at: 23:07:29 rms-change max change #iterations 3.534675 191.6674 at 10iterations 1.469017 70.88654 at 20iterations 0.6123770 22.88017 at 30iterations 0.2562678 9.312466 at 40iterations 0.1066645 4.066256 at 50iterations 4.4894014E-02 1.622816 at 60iterations 1.8738126E-02 0.6459656 at 70iterations 7.8729913E-03 0.2727089 at 80iterations 3.2997136E-03 0.1249084 at 90iterations 1.3847471E-03 5.2685738E-02 at 100iterations 5.8130216E-04 2.1438599E-02 at 110iterations 2.4545786E-04 7.9946518E-03 at 120iterations finished qdiffx linear iterations at : 23:07:37 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 2.4545786E-04 7.9946518E-03 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 23:07:37 7.929u 0.706s 0:09.06 95.1% 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 Sun Oct 9 2011 at 23:07:37 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3470 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: 2.414796 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): -46.77900 10.56700 ymin,ymax (A): -20.76100 45.58000 zmin,zma (A): -93.80200 -32.92700 x,y,z range (A): 57.34600 66.34100 60.87500 scale (grids/A): 2.414796 object centre (A): -18.10600 12.40950 -63.36450 number of atom coordinates read : 3470 total number of charged atoms : 3321 net assigned charge : 8.500010 assigned positive charge : 531.1578 centred at (gu) : 94.03221 84.73924 90.04712 assigned negative charge : -522.6595 centred at (gu) : 94.83804 84.74892 90.24350 start vw surface at 0.1100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 166025 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36571 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 70534 mr = 108583 m= 19636 mr = 52606 m= 3059 mr = 13871 m= 213 mr = 1701 m= 2 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 534 time to turn everything in is 0.8800000 number of dielectric boundary points 82625 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 50 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 26508 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) : 1.609864 object centre at (A) : -18.10600 12.40950 -63.36450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4653395 7.9128243E-02 midg,1,midg; midg,igrid,midg 0.3530886 -0.1359822 1,midg,midg; igrid,midg,midg 8.0298848E-02 -0.2532051 gauss-seidel spectral radius is 0.9991752 estimated iterations to convergence 275 setup time was (sec) 1.140000 now iterating at: 23:07:39 rms-change max change #iterations 9.432890 305.5184 at 10iterations 5.446079 147.0803 at 20iterations 3.117986 89.54211 at 30iterations 1.780481 51.35052 at 40iterations 1.007522 22.53482 at 50iterations 0.5700390 16.30530 at 60iterations 0.3206555 6.779802 at 70iterations 0.1806424 3.992644 at 80iterations 0.1011336 2.492764 at 90iterations 5.6731127E-02 1.294621 at 100iterations 3.1744540E-02 0.6775398 at 110iterations 1.7779635E-02 0.3670292 at 120iterations 9.9159107E-03 0.2057199 at 130iterations 5.5294172E-03 0.1208496 at 140iterations 3.0982376E-03 7.4062347E-02 at 150iterations 1.7275052E-03 3.3711910E-02 at 160iterations 9.6401590E-04 1.7898560E-02 at 170iterations 5.3800037E-04 1.2712479E-02 at 180iterations finished qdiffx linear iterations at : 23:07:51 total time elapsed so far: 13.76000 # loops : 180 mean,max change (kT/e) : 5.3800037E-04 1.2712479E-02 energy calculations done at 13.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.89000 DelPhi exited at 23:07:52 13.896u 0.285s 0:14.46 97.9% 0+0k 0+0io 0pf+0w