Mon Oct 10 10:54:54 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+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 10:54:54 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5335 !!! WARNING: ADP 1609 has a net charge of -2.0000 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: 0.5272824 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): -20.50800 47.00800 ymin,ymax (A): -28.11500 32.82900 zmin,zma (A): -19.78200 45.91700 x,y,z range (A): 67.51601 60.94400 65.69900 scale (grids/A): 0.5272824 object centre (A): 13.25000 2.356999 13.06750 number of atom coordinates read : 5335 total number of charged atoms : 5180 net assigned charge : 9.500031 assigned positive charge : 846.2852 centred at (gu) : 90.83631 89.46345 88.92902 assigned negative charge : -836.7930 centred at (gu) : 90.81920 89.43203 88.98992 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 9537 nv = 96 ne = 84 npr = 105336 no. pairs analyzed = 105336 no. exposed pairs = 6435 no. arc points = 43227 no. surface atoms = 2175 nbur = 3160 mkacc time = 0.1900000 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 = 1.624000 m= 407 mr = 5329 m= 0 mr = 6 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 4609 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4444 ## 613 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 12753 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.3995860E-10 -7.2466040E-11 midg,1,midg; midg,igrid,midg 9.1772021E-11 4.0345449E-10 1,midg,midg; igrid,midg,midg 1.3803905E-10 4.6424628E-10 gauss-seidel spectral radius is 0.9816375 estimated iterations to convergence 61 setup time was (sec) 0.5400000 now iterating at: 10:54:54 rms-change max change #iterations 8.5825428E-02 12.04458 at 10iterations 5.5289268E-03 0.7512598 at 20iterations 9.0311741E-04 0.1297207 at 30iterations 4.3660222E-04 6.4988613E-02 at 40iterations 2.3082097E-04 3.3814430E-02 at 50iterations finished qdiffx linear iterations at : 10:54:57 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 2.3082097E-04 3.3814430E-02 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 10:54:58 3.608u 0.171s 0:04.07 92.6% 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 10:54:58 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5335 !!! WARNING: ADP 1609 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.581847 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): -20.50800 47.00800 ymin,ymax (A): -28.11500 32.82900 zmin,zma (A): -19.78200 45.91700 x,y,z range (A): 67.51601 60.94400 65.69900 scale (grids/A): 1.581847 object centre (A): 13.25000 2.356999 13.06750 number of atom coordinates read : 5335 total number of charged atoms : 5180 net assigned charge : 9.500031 assigned positive charge : 846.2852 centred at (gu) : 92.50725 88.38861 86.78564 assigned negative charge : -836.7930 centred at (gu) : 92.45751 88.29601 86.96976 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 108747 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43227 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 34300 mr = 77901 m= 3183 mr = 24060 m= 78 mr = 1476 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 791 time to turn everything in is 0.5200000 number of dielectric boundary points 42863 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 581 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 39286 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) : 0.5272824 object centre at (A) : 13.25000 2.356999 13.06750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8493906E-03 -4.2275477E-02 midg,1,midg; midg,igrid,midg 3.5356472E-03 6.2020654E-03 1,midg,midg; igrid,midg,midg 2.9429298E-02 1.0392201E-02 gauss-seidel spectral radius is 0.9982870 estimated iterations to convergence 192 setup time was (sec) 0.7400000 now iterating at: 10:54:59 rms-change max change #iterations 4.443671 207.9010 at 10iterations 1.898637 70.04356 at 20iterations 0.8130605 25.52182 at 30iterations 0.3482641 10.25293 at 40iterations 0.1493818 4.648796 at 50iterations 6.4012215E-02 1.914118 at 60iterations 2.7579045E-02 0.7927080 at 70iterations 1.1882402E-02 0.3342381 at 80iterations 5.2094343E-03 0.1484070 at 90iterations 2.3692460E-03 8.3446503E-02 at 100iterations 1.1965047E-03 4.1414261E-02 at 110iterations 7.1968685E-04 2.4046898E-02 at 120iterations finished qdiffx linear iterations at : 10:55:06 total time elapsed so far: 8.020000 # loops : 120 mean,max change (kT/e) : 7.1968685E-04 2.4046898E-02 energy calculations done at 8.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.160000 DelPhi exited at 10:55:06 8.162u 0.204s 0:08.73 95.7% 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 10:55:07 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5335 !!! WARNING: ADP 1609 has a net charge of -2.0000 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: 2.372771 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): -20.50800 47.00800 ymin,ymax (A): -28.11500 32.82900 zmin,zma (A): -19.78200 45.91700 x,y,z range (A): 67.51601 60.94400 65.69900 scale (grids/A): 2.372771 object centre (A): 13.25000 2.356999 13.06750 number of atom coordinates read : 5335 total number of charged atoms : 5180 net assigned charge : 9.500031 assigned positive charge : 846.2852 centred at (gu) : 93.76031 87.58253 85.17824 assigned negative charge : -836.7930 centred at (gu) : 93.68638 87.44409 85.45467 start vw surface at 0.1400000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 252982 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43227 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 121254 mr = 190072 m= 32929 mr = 97652 m= 4758 mr = 24620 m= 300 mr = 3023 m= 6 mr = 107 m= 0 mr = 0 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 2520 time to turn everything in is 1.290000 number of dielectric boundary points 96755 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 64 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 41339 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) : 1.581847 object centre at (A) : 13.25000 2.356999 13.06750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0937193E-02 -1.143286 midg,1,midg; midg,igrid,midg -1.7284650E-02 6.2842466E-02 1,midg,midg; igrid,midg,midg 0.6199721 0.1019866 gauss-seidel spectral radius is 0.9992167 estimated iterations to convergence 282 setup time was (sec) 1.530000 now iterating at: 10:55:08 rms-change max change #iterations 11.79331 327.8860 at 10iterations 6.895136 176.6039 at 20iterations 4.005102 87.18195 at 30iterations 2.307083 48.04510 at 40iterations 1.326702 23.83773 at 50iterations 0.7600406 14.76929 at 60iterations 0.4343630 7.558102 at 70iterations 0.2471942 4.723017 at 80iterations 0.1409143 2.460789 at 90iterations 7.9947390E-02 1.314018 at 100iterations 4.5497749E-02 0.7429552 at 110iterations 2.5879571E-02 0.4567223 at 120iterations 1.4667924E-02 0.2567062 at 130iterations 8.3254445E-03 0.1389732 at 140iterations 4.7316896E-03 8.0970764E-02 at 150iterations 2.6820966E-03 4.2709351E-02 at 160iterations 1.5228287E-03 2.7305603E-02 at 170iterations 8.6758746E-04 1.4511108E-02 at 180iterations finished qdiffx linear iterations at : 10:55:20 total time elapsed so far: 13.20000 # loops : 180 mean,max change (kT/e) : 8.6758746E-04 1.4511108E-02 energy calculations done at 13.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.34000 DelPhi exited at 10:55:20 13.338u 0.214s 0:13.96 96.9% 0+0k 0+0io 0pf+0w