Wed Feb 15 08:55:08 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:55:08 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 ! Automatically converted by prot2crg.py # of charge parameter records: 294 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= 7.9999998E-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 : 7.5399876E-06 assigned positive charge : 351.7182 centred at (gu) : 91.63332 91.32357 88.61794 assigned negative charge : -351.7189 centred at (gu) : 91.65425 91.20290 88.77842 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6497 nv = 96 ne = 84 npr = 49164 no. pairs analyzed = 49164 no. exposed pairs = 3096 no. arc points = 22430 no. surface atoms = 1036 nbur = 1357 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 357 mr = 3397 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.2900000 number of dielectric boundary points 3430 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2266 ## 214 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7844 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8214454E-08 -1.0743515E-08 midg,1,midg; midg,igrid,midg -8.2058911E-09 1.3471847E-08 1,midg,midg; igrid,midg,midg 1.0482607E-09 -3.0877609E-09 gauss-seidel spectral radius is 0.9870659 estimated iterations to convergence 72 setup time was (sec) 0.5000000 now iterating at: 08:55:09 rms-change max change #iterations 0.1299814 21.92909 at 10iterations 1.2490042E-02 1.969465 at 20iterations 1.2015793E-03 0.1988106 at 30iterations 1.1350644E-04 1.7204285E-02 at 40iterations 1.0973095E-05 1.5707016E-03 at 50iterations finished qdiffx linear iterations at : 08:55:12 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 1.0973095E-05 1.5707016E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 08:55:12 3.122u 0.163s 0:03.72 88.1% 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 Wed Feb 15 2012 at 08:55:12 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 ! Automatically converted by prot2crg.py # of charge parameter records: 294 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= 7.9999998E-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 : 7.5399876E-06 assigned positive charge : 351.7182 centred at (gu) : 94.89947 93.97029 85.85341 assigned negative charge : -351.7189 centred at (gu) : 94.96266 93.60883 86.33530 start vw surface at 0.1900000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 69577 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22430 grid for indexing accessible points = 1.400000 m= 25085 mr = 46648 m= 3867 mr = 18049 m= 207 mr = 2312 m= 3 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 495 time to turn everything in is 0.5600000 number of dielectric boundary points 31678 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 128 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 17671 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 2.8741268E-02 -6.1604019E-02 midg,1,midg; midg,igrid,midg -1.1497130E-02 5.9161065E-03 1,midg,midg; igrid,midg,midg 8.7653277E-03 -8.3247747E-04 gauss-seidel spectral radius is 0.9986085 estimated iterations to convergence 212 setup time was (sec) 0.8500000 now iterating at: 08:55:13 rms-change max change #iterations 3.970919 172.1622 at 10iterations 1.841177 66.79243 at 20iterations 0.8541573 29.21133 at 30iterations 0.3973841 14.48794 at 40iterations 0.1831887 5.969719 at 50iterations 8.5633941E-02 2.836370 at 60iterations 3.9628435E-02 1.238371 at 70iterations 1.8416667E-02 0.6439743 at 80iterations 8.5794879E-03 0.3014126 at 90iterations 3.9763199E-03 0.1273499 at 100iterations 1.8428609E-03 6.2670708E-02 at 110iterations 8.5833477E-04 2.8619766E-02 at 120iterations finished qdiffx linear iterations at : 08:55:19 total time elapsed so far: 6.780000 # loops : 120 mean,max change (kT/e) : 8.5833477E-04 2.8619766E-02 energy calculations done at 6.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.960000 DelPhi exited at 08:55:20 6.960u 0.201s 0:07.49 95.5% 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 Wed Feb 15 2012 at 08:55:20 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 ! Automatically converted by prot2crg.py # of charge parameter records: 294 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= 7.0000000E-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 : 7.5399876E-06 assigned positive charge : 351.7182 centred at (gu) : 97.34908 95.95517 83.78001 assigned negative charge : -351.7189 centred at (gu) : 97.44394 95.41316 84.50285 start vw surface at 0.1400000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 160395 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22430 grid for indexing accessible points = 1.400000 m= 79721 mr = 112789 m= 29530 mr = 64252 m= 6932 mr = 23278 m= 861 mr = 5040 m= 34 mr = 515 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 1871 time to turn everything in is 1.230000 number of dielectric boundary points 71590 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.360000 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 0.2700208 -0.7448371 midg,1,midg; midg,igrid,midg -0.1000879 3.0414691E-02 1,midg,midg; igrid,midg,midg 9.6787073E-02 -2.6006659E-02 gauss-seidel spectral radius is 0.9992566 estimated iterations to convergence 289 setup time was (sec) 1.530000 now iterating at: 08:55:22 rms-change max change #iterations 9.445438 361.5969 at 10iterations 5.506371 128.9042 at 20iterations 3.186935 92.52051 at 30iterations 1.840078 37.45496 at 40iterations 1.061449 21.16433 at 50iterations 0.6118652 13.07093 at 60iterations 0.3522489 8.306401 at 70iterations 0.2021351 4.114440 at 80iterations 0.1161929 2.256745 at 90iterations 6.6699319E-02 1.358209 at 100iterations 3.8360979E-02 0.7614670 at 110iterations 2.1954114E-02 0.4062042 at 120iterations 1.2559593E-02 0.2335112 at 130iterations 7.2170189E-03 0.1369336 at 140iterations 4.1431114E-03 7.5095177E-02 at 150iterations 2.3745075E-03 4.4054031E-02 at 160iterations 1.3590499E-03 2.4610519E-02 at 170iterations 7.8189565E-04 1.4339447E-02 at 180iterations finished qdiffx linear iterations at : 08:55:33 total time elapsed so far: 12.60000 # loops : 180 mean,max change (kT/e) : 7.8189565E-04 1.4339447E-02 energy calculations done at 12.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.79000 DelPhi exited at 08:55:33 12.789u 0.264s 0:13.65 95.5% 0+0k 0+0io 0pf+0w