Tue Oct 11 03:16:41 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 Tue Oct 11 2011 at 03:16:41 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2393 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: 0.6331590 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): -28.02200 21.85300 ymin,ymax (A): -24.85600 24.13500 zmin,zma (A): -23.95600 32.27000 x,y,z range (A): 49.87500 48.99100 56.22600 scale (grids/A): 0.6331590 object centre (A): -3.084499 -0.3605003 4.157001 number of atom coordinates read : 2393 total number of charged atoms : 2248 net assigned charge : 1.000010 assigned positive charge : 353.3181 centred at (gu) : 91.63002 91.33067 88.64338 assigned negative charge : -352.3189 centred at (gu) : 91.66038 91.21992 88.79911 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6525 nv = 96 ne = 84 npr = 48199 no. pairs analyzed = 48199 no. exposed pairs = 3046 no. arc points = 22119 no. surface atoms = 1023 nbur = 1370 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 354 mr = 3457 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.3300000 number of dielectric boundary points 3393 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2239 ## 212 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7840 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9225958E-08 -9.5804653E-09 midg,1,midg; midg,igrid,midg -6.6175270E-09 1.3999943E-08 1,midg,midg; igrid,midg,midg 2.4947018E-09 -2.5557492E-09 gauss-seidel spectral radius is 0.9870663 estimated iterations to convergence 72 setup time was (sec) 0.6000000 now iterating at: 03:16:42 rms-change max change #iterations 0.1330316 21.15133 at 10iterations 1.2821320E-02 2.085503 at 20iterations 1.2309533E-03 0.1639454 at 30iterations 1.1770941E-04 1.6456604E-02 at 40iterations 1.1366281E-05 1.6853809E-03 at 50iterations finished qdiffx linear iterations at : 03:16:45 total time elapsed so far: 3.880000 # loops : 50 mean,max change (kT/e) : 1.1366281E-05 1.6853809E-03 energy calculations done at 3.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.060000 DelPhi exited at 03:16:46 4.061u 0.259s 0:04.66 92.4% 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 03:16:46 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2393 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: 1.899477 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): -28.02200 21.85300 ymin,ymax (A): -24.85600 24.13500 zmin,zma (A): -23.95600 32.27000 x,y,z range (A): 49.87500 48.99100 56.22600 scale (grids/A): 1.899477 object centre (A): -3.084499 -0.3605003 4.157001 number of atom coordinates read : 2393 total number of charged atoms : 2248 net assigned charge : 1.000010 assigned positive charge : 353.3181 centred at (gu) : 94.88956 93.99155 85.92982 assigned negative charge : -352.3189 centred at (gu) : 94.98103 93.65987 86.39735 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 70180 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22119 grid for indexing accessible points = 1.400000 m= 25222 mr = 47539 m= 3826 mr = 18264 m= 200 mr = 2277 m= 3 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 741 time to turn everything in is 0.6300000 number of dielectric boundary points 31305 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 125 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 17660 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) : 0.6331590 object centre at (A) : -3.084499 -0.3605003 4.157001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3177659E-02 -6.1225545E-02 midg,1,midg; midg,igrid,midg -1.0282609E-02 8.5845431E-03 1,midg,midg; igrid,midg,midg 1.0909430E-02 -1.3346772E-03 gauss-seidel spectral radius is 0.9986078 estimated iterations to convergence 212 setup time was (sec) 0.9300000 now iterating at: 03:16:47 rms-change max change #iterations 3.993319 172.1296 at 10iterations 1.849862 66.76778 at 20iterations 0.8590060 27.92296 at 30iterations 0.3995870 14.02365 at 40iterations 0.1843685 5.953781 at 50iterations 8.6224422E-02 2.987423 at 60iterations 3.9924555E-02 1.292458 at 70iterations 1.8530387E-02 0.6063318 at 80iterations 8.6395284E-03 0.2948761 at 90iterations 4.0013599E-03 0.1268805 at 100iterations 1.8527959E-03 6.6657066E-02 at 110iterations 8.6402969E-04 3.1295776E-02 at 120iterations finished qdiffx linear iterations at : 03:16:55 total time elapsed so far: 9.260000 # loops : 120 mean,max change (kT/e) : 8.6402969E-04 3.1295776E-02 energy calculations done at 9.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.440000 DelPhi exited at 03:16:56 9.441u 0.311s 0:10.39 93.8% 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 03:16:56 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2393 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: 2.849216 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): -28.02200 21.85300 ymin,ymax (A): -24.85600 24.13500 zmin,zma (A): -23.95600 32.27000 x,y,z range (A): 49.87500 48.99100 56.22600 scale (grids/A): 2.849216 object centre (A): -3.084499 -0.3605003 4.157001 number of atom coordinates read : 2393 total number of charged atoms : 2248 net assigned charge : 1.000010 assigned positive charge : 353.3181 centred at (gu) : 97.33421 95.98708 83.89457 assigned negative charge : -352.3189 centred at (gu) : 97.47147 95.48973 84.59592 start vw surface at 0.1500000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 161822 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22119 grid for indexing accessible points = 1.400000 m= 80415 mr = 114773 m= 29611 mr = 65144 m= 6840 mr = 23439 m= 836 mr = 4970 m= 32 mr = 485 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 2576 time to turn everything in is 1.600000 number of dielectric boundary points 70736 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 17983 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) : 1.899477 object centre at (A) : -3.084499 -0.3605003 4.157001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3224201 -0.7405069 midg,1,midg; midg,igrid,midg -8.6465940E-02 5.9167452E-02 1,midg,midg; igrid,midg,midg 0.1181707 -3.1054085E-02 gauss-seidel spectral radius is 0.9992537 estimated iterations to convergence 289 setup time was (sec) 1.930000 now iterating at: 03:16:58 rms-change max change #iterations 9.434021 361.2255 at 10iterations 5.471457 124.7038 at 20iterations 3.155051 96.27811 at 30iterations 1.817841 37.12889 at 40iterations 1.045011 21.56159 at 50iterations 0.6015806 12.67383 at 60iterations 0.3452375 7.488714 at 70iterations 0.1974728 3.957314 at 80iterations 0.1134515 2.165580 at 90iterations 6.5080613E-02 1.301427 at 100iterations 3.7285052E-02 0.7488260 at 110iterations 2.1370646E-02 0.4020090 at 120iterations 1.2212815E-02 0.2136078 at 130iterations 6.9968179E-03 0.1262846 at 140iterations 4.0074657E-03 7.4038506E-02 at 150iterations 2.2944578E-03 4.6510458E-02 at 160iterations 1.3136326E-03 2.7063370E-02 at 170iterations 7.5302366E-04 1.5913010E-02 at 180iterations finished qdiffx linear iterations at : 03:17:12 total time elapsed so far: 15.57000 # loops : 180 mean,max change (kT/e) : 7.5302366E-04 1.5913010E-02 energy calculations done at 15.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.75000 DelPhi exited at 03:17:13 15.747u 0.306s 0:16.60 96.6% 0+0k 0+0io 0pf+0w