Tue Oct 11 08:00:22 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 08:00:22 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 = 2517 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: 0.5426415 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): -17.28600 27.87300 ymin,ymax (A): -3.805000 52.75100 zmin,zma (A): 7.289999 72.89500 x,y,z range (A): 45.15900 56.55600 65.60500 scale (grids/A): 0.5426415 object centre (A): 5.293500 24.47300 40.09250 number of atom coordinates read : 2517 total number of charged atoms : 2376 net assigned charge : 11.00002 assigned positive charge : 370.4078 centred at (gu) : 88.79944 90.38187 91.89404 assigned negative charge : -359.4086 centred at (gu) : 88.72392 90.34354 91.70926 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 4870 nv = 96 ne = 84 npr = 48893 no. pairs analyzed = 48893 no. exposed pairs = 3390 no. arc points = 24336 no. surface atoms = 1135 nbur = 1382 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 = 1.568000 m= 192 mr = 2307 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 2751 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2491 ## 343 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 6322 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8320526E-10 2.3072049E-09 midg,1,midg; midg,igrid,midg 3.6733910E-10 8.3788226E-10 1,midg,midg; igrid,midg,midg 2.9282471E-10 6.9830358E-10 gauss-seidel spectral radius is 0.9824666 estimated iterations to convergence 62 setup time was (sec) 0.3700000 now iterating at: 08:00:23 rms-change max change #iterations 6.2889524E-02 12.43357 at 10iterations 3.9568390E-03 0.7355156 at 20iterations 2.5801931E-04 5.1368713E-02 at 30iterations 1.7369079E-05 4.0636063E-03 at 40iterations 1.1655113E-06 2.0599365E-04 at 50iterations finished qdiffx linear iterations at : 08:00:26 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 1.1655113E-06 2.0599365E-04 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 08:00:26 3.424u 0.192s 0:03.91 92.3% 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 08:00:26 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2517 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: 1.627925 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): -17.28600 27.87300 ymin,ymax (A): -3.805000 52.75100 zmin,zma (A): 7.289999 72.89500 x,y,z range (A): 45.15900 56.55600 65.60500 scale (grids/A): 1.627925 object centre (A): 5.293500 24.47300 40.09250 number of atom coordinates read : 2517 total number of charged atoms : 2376 net assigned charge : 11.00002 assigned positive charge : 370.4078 centred at (gu) : 86.39769 91.14491 95.68160 assigned negative charge : -359.4086 centred at (gu) : 86.17152 91.03036 95.12744 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 54138 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24336 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 15028 mr = 34593 m= 1402 mr = 9747 m= 39 mr = 647 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 207 time to turn everything in is 0.2900000 number of dielectric boundary points 25620 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 319 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 18151 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) : 0.5426415 object centre at (A) : 5.293500 24.47300 40.09250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4007704E-02 5.8490064E-02 midg,1,midg; midg,igrid,midg 4.8666787E-03 6.6295550E-03 1,midg,midg; igrid,midg,midg 6.4644841E-03 7.8235408E-03 gauss-seidel spectral radius is 0.9981270 estimated iterations to convergence 184 setup time was (sec) 0.5100000 now iterating at: 08:00:27 rms-change max change #iterations 2.911255 153.9157 at 10iterations 1.191508 57.44989 at 20iterations 0.4867056 19.39263 at 30iterations 0.1993172 8.276482 at 40iterations 8.1364222E-02 3.317612 at 50iterations 3.3590045E-02 1.312748 at 60iterations 1.3771251E-02 0.6165771 at 70iterations 5.6336350E-03 0.2167358 at 80iterations 2.3269022E-03 9.8786354E-02 at 90iterations 9.5108448E-04 4.4223785E-02 at 100iterations 3.8987305E-04 1.5792847E-02 at 110iterations 1.6106176E-04 6.8368912E-03 at 120iterations finished qdiffx linear iterations at : 08:00:34 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 1.6106176E-04 6.8368912E-03 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 08:00:34 7.761u 0.188s 0:08.27 96.0% 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 08:00:34 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 = 2517 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: 2.441887 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): -17.28600 27.87300 ymin,ymax (A): -3.805000 52.75100 zmin,zma (A): 7.289999 72.89500 x,y,z range (A): 45.15900 56.55600 65.60500 scale (grids/A): 2.441887 object centre (A): 5.293500 24.47300 40.09250 number of atom coordinates read : 2517 total number of charged atoms : 2376 net assigned charge : 11.00002 assigned positive charge : 370.4078 centred at (gu) : 84.59631 91.71734 98.52217 assigned negative charge : -359.4086 centred at (gu) : 84.25710 91.54552 97.69112 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 125749 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24336 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 53176 mr = 85296 m= 13784 mr = 40803 m= 2074 mr = 9701 m= 127 mr = 1258 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 751 time to turn everything in is 0.6500000 number of dielectric boundary points 57813 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 29 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 18981 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) : 1.627925 object centre at (A) : 5.293500 24.47300 40.09250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1213381 1.222717 midg,1,midg; midg,igrid,midg 4.8101019E-02 4.9138404E-02 1,midg,midg; igrid,midg,midg 8.3829187E-02 0.1033051 gauss-seidel spectral radius is 0.9991075 estimated iterations to convergence 264 setup time was (sec) 0.8800000 now iterating at: 08:00:36 rms-change max change #iterations 7.562715 288.0200 at 10iterations 4.185118 122.1451 at 20iterations 2.298734 59.04212 at 30iterations 1.258745 29.63379 at 40iterations 0.6897396 15.60537 at 50iterations 0.3747847 8.899961 at 60iterations 0.2038998 4.460938 at 70iterations 0.1108430 2.402898 at 80iterations 6.0134210E-02 1.331734 at 90iterations 3.2695394E-02 0.7195768 at 100iterations 1.7751109E-02 0.4491129 at 110iterations 9.6283369E-03 0.2144127 at 120iterations 5.2274456E-03 0.1142769 at 130iterations 2.8331447E-03 6.0630798E-02 at 140iterations 1.5393075E-03 3.4033775E-02 at 150iterations 8.3562225E-04 1.8032074E-02 at 160iterations 4.5261552E-04 1.0978699E-02 at 170iterations 2.4563697E-04 5.5077076E-03 at 180iterations finished qdiffx linear iterations at : 08:00:47 total time elapsed so far: 12.15000 # loops : 180 mean,max change (kT/e) : 2.4563697E-04 5.5077076E-03 energy calculations done at 12.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.28000 DelPhi exited at 08:00:47 12.283u 0.223s 0:12.95 96.5% 0+0k 0+0io 0pf+0w