Mon Oct 10 17:09:29 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 17:09:29 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2774 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5821273 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): 1.791000 62.94600 ymin,ymax (A): 11.97400 63.11200 zmin,zma (A): -7.338000 41.99000 x,y,z range (A): 61.15500 51.13800 49.32800 scale (grids/A): 0.5821273 object centre (A): 32.36850 37.54300 17.32600 number of atom coordinates read : 2774 total number of charged atoms : 2635 net assigned charge : -1.485975 assigned positive charge : 418.5752 centred at (gu) : 89.85077 88.91279 89.04498 assigned negative charge : -420.0623 centred at (gu) : 89.92171 89.16615 88.89674 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6231 nv = 96 ne = 84 npr = 54367 no. pairs analyzed = 54367 no. exposed pairs = 3736 no. arc points = 26464 no. surface atoms = 1258 nbur = 1516 mkacc time = 9.0000004E-02 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 = 1.484000 m= 278 mr = 3102 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3384 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2610 ## 269 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7859 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6903463E-09 2.2890840E-09 midg,1,midg; midg,igrid,midg 6.6252115E-09 -4.7926245E-09 1,midg,midg; igrid,midg,midg 1.2373365E-09 -1.9000712E-09 gauss-seidel spectral radius is 0.9847587 estimated iterations to convergence 67 setup time was (sec) 0.3800000 now iterating at: 17:09:30 rms-change max change #iterations 9.8752789E-02 16.38704 at 10iterations 7.5753140E-03 1.337484 at 20iterations 6.1559002E-04 7.8695774E-02 at 30iterations 5.3690994E-05 1.0100365E-02 at 40iterations 6.7308470E-06 1.1725426E-03 at 50iterations finished qdiffx linear iterations at : 17:09:33 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 6.7308470E-06 1.1725426E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 17:09:33 3.369u 0.170s 0:03.89 90.7% 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 17:09:33 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2774 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.746382 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): 1.791000 62.94600 ymin,ymax (A): 11.97400 63.11200 zmin,zma (A): -7.338000 41.99000 x,y,z range (A): 61.15500 51.13800 49.32800 scale (grids/A): 1.746382 object centre (A): 32.36850 37.54300 17.32600 number of atom coordinates read : 2774 total number of charged atoms : 2635 net assigned charge : -1.485975 assigned positive charge : 418.5752 centred at (gu) : 89.55160 86.73742 87.13399 assigned negative charge : -420.0623 centred at (gu) : 89.76475 87.49792 86.68993 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 68669 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26464 grid for indexing accessible points = 1.400000 m= 21306 mr = 45583 m= 2453 mr = 14375 m= 96 mr = 1199 m= 1 mr = 12 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 0.3300000 number of dielectric boundary points 31356 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 246 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 20474 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) : 0.5821273 object centre at (A) : 32.36850 37.54300 17.32600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.3290888E-03 1.4508991E-03 midg,1,midg; midg,igrid,midg 2.0881863E-02 -2.2242559E-02 1,midg,midg; igrid,midg,midg 1.2487791E-02 -3.9812364E-03 gauss-seidel spectral radius is 0.9984100 estimated iterations to convergence 199 setup time was (sec) 0.5300000 now iterating at: 17:09:34 rms-change max change #iterations 3.727389 167.9929 at 10iterations 1.637475 67.32320 at 20iterations 0.7199052 24.65381 at 30iterations 0.3170102 10.92070 at 40iterations 0.1396433 4.726185 at 50iterations 6.1670378E-02 2.043275 at 60iterations 2.7135221E-02 0.9152203 at 70iterations 1.1985746E-02 0.4362879 at 80iterations 5.2851662E-03 0.1989632 at 90iterations 2.3402139E-03 8.0013275E-02 at 100iterations 1.0292089E-03 3.6187649E-02 at 110iterations 4.5313183E-04 1.6693115E-02 at 120iterations finished qdiffx linear iterations at : 17:09:41 total time elapsed so far: 7.460000 # loops : 120 mean,max change (kT/e) : 4.5313183E-04 1.6693115E-02 energy calculations done at 7.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.590000 DelPhi exited at 17:09:41 7.589u 0.200s 0:08.08 96.2% 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 Mon Oct 10 2011 at 17:09:41 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2774 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.619573 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): 1.791000 62.94600 ymin,ymax (A): 11.97400 63.11200 zmin,zma (A): -7.338000 41.99000 x,y,z range (A): 61.15500 51.13800 49.32800 scale (grids/A): 2.619573 object centre (A): 32.36850 37.54300 17.32600 number of atom coordinates read : 2774 total number of charged atoms : 2635 net assigned charge : -1.485975 assigned positive charge : 418.5752 centred at (gu) : 89.32744 85.10583 85.70093 assigned negative charge : -420.0623 centred at (gu) : 89.64707 86.24677 85.03481 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 159208 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26464 grid for indexing accessible points = 1.400000 m= 72010 mr = 111381 m= 21654 mr = 56138 m= 3934 mr = 16093 m= 335 mr = 2602 m= 6 mr = 169 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8300000 number of dielectric boundary points 70764 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 21076 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) : 1.746382 object centre at (A) : 32.36850 37.54300 17.32600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.1806133E-02 3.1579116E-03 midg,1,midg; midg,igrid,midg 0.2767680 -0.2666518 1,midg,midg; igrid,midg,midg 0.1796986 6.4916186E-02 gauss-seidel spectral radius is 0.9992096 estimated iterations to convergence 281 setup time was (sec) 1.060000 now iterating at: 17:09:43 rms-change max change #iterations 9.329973 366.6845 at 10iterations 5.377038 142.3826 at 20iterations 3.089994 82.71327 at 30iterations 1.763953 38.80435 at 40iterations 1.002332 25.40290 at 50iterations 0.5705270 13.53268 at 60iterations 0.3243067 7.259378 at 70iterations 0.1836692 3.845480 at 80iterations 0.1039966 2.456559 at 90iterations 5.8595613E-02 1.256834 at 100iterations 3.3196591E-02 0.7433686 at 110iterations 1.8729560E-02 0.3802118 at 120iterations 1.0587579E-02 0.2197671 at 130iterations 5.9710494E-03 0.1177516 at 140iterations 3.3677150E-03 7.0509911E-02 at 150iterations 1.8995984E-03 3.7062168E-02 at 160iterations 1.0713870E-03 2.2003174E-02 at 170iterations 6.0426554E-04 1.2229443E-02 at 180iterations finished qdiffx linear iterations at : 17:09:54 total time elapsed so far: 12.04000 # loops : 180 mean,max change (kT/e) : 6.0426554E-04 1.2229443E-02 energy calculations done at 12.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.17000 DelPhi exited at 17:09:54 12.173u 0.189s 0:12.83 96.2% 0+0k 0+0io 0pf+0w