Sun Oct 9 19:32:20 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 Sun Oct 9 2011 at 19:32:20 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3053 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5189655 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): -3.137000 65.46100 ymin,ymax (A): -13.64100 35.11400 zmin,zma (A): 18.81300 71.04800 x,y,z range (A): 68.59800 48.75500 52.23500 scale (grids/A): 0.5189655 object centre (A): 31.16200 10.73650 44.93050 number of atom coordinates read : 3053 total number of charged atoms : 2910 net assigned charge : 11.50003 assigned positive charge : 464.9442 centred at (gu) : 89.92826 89.80489 89.80766 assigned negative charge : -453.4454 centred at (gu) : 90.03382 89.85290 89.79204 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5345 nv = 96 ne = 84 npr = 59933 no. pairs analyzed = 59933 no. exposed pairs = 3988 no. arc points = 28227 no. surface atoms = 1322 nbur = 1731 mkacc time = 0.1400000 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 = 1.652000 m= 212 mr = 2688 m= 3 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 2870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2786 ## 420 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7080 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0876730E-10 2.5927241E-10 midg,1,midg; midg,igrid,midg 3.6531006E-10 1.1677956E-10 1,midg,midg; igrid,midg,midg 4.8867493E-10 -1.4786604E-11 gauss-seidel spectral radius is 0.9808860 estimated iterations to convergence 60 setup time was (sec) 0.5600000 now iterating at: 19:32:21 rms-change max change #iterations 5.6901116E-02 11.42576 at 10iterations 3.4469250E-03 0.5952950 at 20iterations 4.4819861E-04 8.5652351E-02 at 30iterations 1.5977626E-04 2.6021004E-02 at 40iterations 6.6099725E-05 1.0691643E-02 at 50iterations finished qdiffx linear iterations at : 19:32:24 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 6.6099725E-05 1.0691643E-02 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 19:32:24 3.368u 0.157s 0:03.80 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 Sun Oct 9 2011 at 19:32:24 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 = 3053 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: 1.556897 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): -3.137000 65.46100 ymin,ymax (A): -13.64100 35.11400 zmin,zma (A): 18.81300 71.04800 x,y,z range (A): 68.59800 48.75500 52.23500 scale (grids/A): 1.556897 object centre (A): 31.16200 10.73650 44.93050 number of atom coordinates read : 3053 total number of charged atoms : 2910 net assigned charge : 11.50003 assigned positive charge : 464.9442 centred at (gu) : 89.78431 89.41344 89.42214 assigned negative charge : -453.4454 centred at (gu) : 90.10146 89.55825 89.37617 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 60001 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28227 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 18717 mr = 40391 m= 1814 mr = 12539 m= 58 mr = 720 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 322 time to turn everything in is 0.4700000 number of dielectric boundary points 26940 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 397 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 21998 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) : 0.5189655 object centre at (A) : 31.16200 10.73650 44.93050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3563491E-03 4.8351423E-03 midg,1,midg; midg,igrid,midg 6.2072277E-03 2.7463438E-03 1,midg,midg; igrid,midg,midg 1.9513663E-02 3.7509631E-03 gauss-seidel spectral radius is 0.9980039 estimated iterations to convergence 178 setup time was (sec) 0.7600000 now iterating at: 19:32:25 rms-change max change #iterations 3.014970 150.3493 at 10iterations 1.203998 53.24248 at 20iterations 0.4793882 19.41696 at 30iterations 0.1915230 7.739385 at 40iterations 7.6668181E-02 3.337595 at 50iterations 3.0676914E-02 1.191203 at 60iterations 1.2321571E-02 0.4533997 at 70iterations 4.9883579E-03 0.1997490 at 80iterations 2.0572895E-03 8.9990139E-02 at 90iterations 9.0205570E-04 3.5467148E-02 at 100iterations 4.5190082E-04 1.7048836E-02 at 110iterations 2.7004618E-04 1.0210991E-02 at 120iterations finished qdiffx linear iterations at : 19:32:32 total time elapsed so far: 7.210000 # loops : 120 mean,max change (kT/e) : 2.7004618E-04 1.0210991E-02 energy calculations done at 7.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.400000 DelPhi exited at 19:32:32 7.407u 0.191s 0:07.88 96.3% 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 Sun Oct 9 2011 at 19:32:32 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 = 3053 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: 2.335345 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): -3.137000 65.46100 ymin,ymax (A): -13.64100 35.11400 zmin,zma (A): 18.81300 71.04800 x,y,z range (A): 68.59800 48.75500 52.23500 scale (grids/A): 2.335345 object centre (A): 31.16200 10.73650 44.93050 number of atom coordinates read : 3053 total number of charged atoms : 2910 net assigned charge : 11.50003 assigned positive charge : 464.9442 centred at (gu) : 89.67615 89.12009 89.13306 assigned negative charge : -453.4454 centred at (gu) : 90.15202 89.33748 89.06422 start vw surface at 0.1500000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 139276 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28227 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 65089 mr = 99270 m= 18091 mr = 50693 m= 2607 mr = 13065 m= 179 mr = 1444 m= 3 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 943 time to turn everything in is 1.100000 number of dielectric boundary points 60703 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 44 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 23239 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) : 1.556897 object centre at (A) : 31.16200 10.73650 44.93050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9727344E-02 7.3322549E-02 midg,1,midg; midg,igrid,midg 9.9719062E-02 3.7454296E-02 1,midg,midg; igrid,midg,midg 0.4073927 8.6729735E-02 gauss-seidel spectral radius is 0.9990796 estimated iterations to convergence 260 setup time was (sec) 1.410000 now iterating at: 19:32:34 rms-change max change #iterations 8.112996 290.9228 at 10iterations 4.488450 145.7299 at 20iterations 2.468398 58.20158 at 30iterations 1.352595 33.16328 at 40iterations 0.7353569 16.63101 at 50iterations 0.4009688 9.962530 at 60iterations 0.2176611 5.129103 at 70iterations 0.1179186 2.959984 at 80iterations 6.4081773E-02 1.646363 at 90iterations 3.4657996E-02 0.9154816 at 100iterations 1.8747155E-02 0.4281549 at 110iterations 1.0141984E-02 0.2369020 at 120iterations 5.4862420E-03 0.1330042 at 130iterations 2.9677078E-03 7.2143078E-02 at 140iterations 1.6093730E-03 4.0149689E-02 at 150iterations 8.7581598E-04 2.2661686E-02 at 160iterations 4.8038573E-04 1.1445999E-02 at 170iterations 2.7068998E-04 6.5174103E-03 at 180iterations finished qdiffx linear iterations at : 19:32:44 total time elapsed so far: 11.51000 # loops : 180 mean,max change (kT/e) : 2.7068998E-04 6.5174103E-03 energy calculations done at 11.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.70000 DelPhi exited at 19:32:44 11.702u 0.209s 0:12.19 97.6% 0+0k 0+0io 0pf+0w