Sat Oct 15 13:16:20 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 Sat Oct 15 2011 at 13:16:20 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: 353 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5384 !!! WARNING: ASL 284 has a net charge of -0.1000 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5021157 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): 3.357000 68.38700 ymin,ymax (A): -8.946000 53.69500 zmin,zma (A): -2.281000 68.61900 x,y,z range (A): 65.03000 62.64100 70.89999 scale (grids/A): 0.5021157 object centre (A): 35.87200 22.37450 33.16900 number of atom coordinates read : 5384 total number of charged atoms : 5226 net assigned charge : 5.654033 assigned positive charge : 831.1952 centred at (gu) : 88.16223 89.34241 88.71295 assigned negative charge : -825.5471 centred at (gu) : 88.08435 89.36964 88.64863 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8703 nv = 96 ne = 84 npr = 108916 no. pairs analyzed = 108916 no. exposed pairs = 6278 no. arc points = 43241 no. surface atoms = 2148 nbur = 3236 mkacc time = 0.2500000 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 = 1.708000 m= 306 mr = 4793 m= 0 mr = 8 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 4208 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4237 ## 583 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 11613 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0705240E-10 1.3509899E-10 midg,1,midg; midg,igrid,midg 1.3701175E-10 2.7552489E-12 1,midg,midg; igrid,midg,midg -1.7245280E-10 1.3356059E-10 gauss-seidel spectral radius is 0.9797564 estimated iterations to convergence 58 setup time was (sec) 0.7900000 now iterating at: 13:16:21 rms-change max change #iterations 7.3037297E-02 9.608547 at 10iterations 9.4027640E-03 1.526455 at 20iterations 3.7737491E-03 0.6786156 at 30iterations 1.6812675E-03 0.3015060 at 40iterations 7.5622363E-04 0.1336136 at 50iterations finished qdiffx linear iterations at : 13:16:25 total time elapsed so far: 4.290000 # loops : 50 mean,max change (kT/e) : 7.5622363E-04 0.1336136 energy calculations done at 4.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.470000 DelPhi exited at 13:16:25 4.478u 0.250s 0:05.17 91.2% 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 13:16:26 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: 353 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5384 !!! WARNING: ASL 284 has a net charge of -0.1000 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.506347 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): 3.357000 68.38700 ymin,ymax (A): -8.946000 53.69500 zmin,zma (A): -2.281000 68.61900 x,y,z range (A): 65.03000 62.64100 70.89999 scale (grids/A): 1.506347 object centre (A): 35.87200 22.37450 33.16900 number of atom coordinates read : 5384 total number of charged atoms : 5226 net assigned charge : 5.654033 assigned positive charge : 831.1952 centred at (gu) : 84.48524 88.02605 86.13757 assigned negative charge : -825.5471 centred at (gu) : 84.25292 88.10873 85.94571 start vw surface at 0.2100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 99022 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43241 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 30709 mr = 70953 m= 2824 mr = 21243 m= 41 mr = 1243 m= 0 mr = 4 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7300000 number of dielectric boundary points 39153 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 572 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 39074 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) : 0.5021157 object centre at (A) : 35.87200 22.37450 33.16900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1205557E-02 1.5643023E-02 midg,1,midg; midg,igrid,midg 1.1839820E-02 4.1520051E-03 1,midg,midg; igrid,midg,midg -9.1992542E-03 4.9615274E-03 gauss-seidel spectral radius is 0.9980828 estimated iterations to convergence 182 setup time was (sec) 1.080000 now iterating at: 13:16:27 rms-change max change #iterations 3.999247 144.2907 at 10iterations 1.626286 51.36400 at 20iterations 0.6638341 19.84129 at 30iterations 0.2709446 8.381336 at 40iterations 0.1115738 3.283798 at 50iterations 4.6774101E-02 1.616089 at 60iterations 2.0687867E-02 0.6852188 at 70iterations 1.0174615E-02 0.3693810 at 80iterations 5.9583881E-03 0.2111092 at 90iterations 3.9365608E-03 0.1354866 at 100iterations 2.8025606E-03 9.3132019E-02 at 110iterations 2.0444936E-03 6.7993164E-02 at 120iterations finished qdiffx linear iterations at : 13:16:36 total time elapsed so far: 10.04000 # loops : 120 mean,max change (kT/e) : 2.0444936E-03 6.7993164E-02 energy calculations done at 10.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.22000 DelPhi exited at 13:16:36 10.226u 0.264s 0:10.81 96.9% 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 13:16:36 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: 353 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5384 !!! WARNING: ASL 284 has a net charge of -0.1000 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.259521 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): 3.357000 68.38700 ymin,ymax (A): -8.946000 53.69500 zmin,zma (A): -2.281000 68.61900 x,y,z range (A): 65.03000 62.64100 70.89999 scale (grids/A): 2.259521 object centre (A): 35.87200 22.37450 33.16900 number of atom coordinates read : 5384 total number of charged atoms : 5226 net assigned charge : 5.654033 assigned positive charge : 831.1952 centred at (gu) : 81.72748 87.03823 84.20615 assigned negative charge : -825.5471 centred at (gu) : 81.37932 87.16306 83.91850 start vw surface at 0.2100000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 230936 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43241 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 109365 mr = 173563 m= 29137 mr = 87743 m= 4034 mr = 21584 m= 209 mr = 2491 m= 0 mr = 72 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.800000 number of dielectric boundary points 88228 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 79 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 41653 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) : 1.506347 object centre at (A) : 35.87200 22.37450 33.16900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3045590 0.5488746 midg,1,midg; midg,igrid,midg 0.2176387 3.3459831E-02 1,midg,midg; igrid,midg,midg -0.2469957 7.6475352E-02 gauss-seidel spectral radius is 0.9991555 estimated iterations to convergence 272 setup time was (sec) 2.170000 now iterating at: 13:16:39 rms-change max change #iterations 10.80556 326.4517 at 10iterations 6.143930 135.5877 at 20iterations 3.463031 72.68004 at 30iterations 1.948809 49.03757 at 40iterations 1.091447 20.33865 at 50iterations 0.6084996 11.90965 at 60iterations 0.3398538 6.165078 at 70iterations 0.1889665 3.582230 at 80iterations 0.1055083 1.859812 at 90iterations 5.8942284E-02 1.040274 at 100iterations 3.3205077E-02 0.6837921 at 110iterations 1.8890632E-02 0.3600216 at 120iterations 1.1050518E-02 0.2499695 at 130iterations 6.7762178E-03 0.1453209 at 140iterations 4.4185170E-03 9.1529846E-02 at 150iterations 3.1128889E-03 6.8447113E-02 at 160iterations 2.3287213E-03 4.8019409E-02 at 170iterations 1.8166513E-03 3.6926270E-02 at 180iterations finished qdiffx linear iterations at : 13:16:53 total time elapsed so far: 16.71000 # loops : 180 mean,max change (kT/e) : 1.8166513E-03 3.6926270E-02 energy calculations done at 16.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.90000 DelPhi exited at 13:16:54 16.904u 0.304s 0:17.77 96.7% 0+0k 0+0io 0pf+0w