Tue Jan 31 10:32:05 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.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 Jan 31 2012 at 10:32:05 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: 950 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3602 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: 0.5626502 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): -2.179000 60.05100 ymin,ymax (A): -18.31500 44.95700 zmin,zma (A): -5.386000 54.96500 x,y,z range (A): 62.23000 63.27200 60.35100 scale (grids/A): 0.5626502 object centre (A): 28.93600 13.32100 24.78950 number of atom coordinates read : 3602 total number of charged atoms : 3455 net assigned charge : -6.999962 assigned positive charge : 540.9139 centred at (gu) : 88.94090 86.26865 91.06756 assigned negative charge : -547.9156 centred at (gu) : 89.01965 86.20721 90.99632 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7367 nv = 96 ne = 84 npr = 74270 no. pairs analyzed = 74270 no. exposed pairs = 4620 no. arc points = 32233 no. surface atoms = 1552 nbur = 2050 mkacc time = 0.1600000 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 = 1.540000 m= 304 mr = 3789 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3865 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3305 ## 404 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 9718 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4324572E-09 3.3129116E-10 midg,1,midg; midg,igrid,midg -4.2442831E-09 2.8144126E-11 1,midg,midg; igrid,midg,midg 4.7079030E-10 -1.5219949E-09 gauss-seidel spectral radius is 0.9837562 estimated iterations to convergence 65 setup time was (sec) 0.5300000 now iterating at: 10:32:06 rms-change max change #iterations 9.3807600E-02 15.66894 at 10iterations 6.9916220E-03 0.9403579 at 20iterations 6.5954740E-04 9.7539425E-02 at 30iterations 1.2901261E-04 2.2782803E-02 at 40iterations 3.6169051E-05 6.4659119E-03 at 50iterations finished qdiffx linear iterations at : 10:32:09 total time elapsed so far: 3.480000 # loops : 50 mean,max change (kT/e) : 3.6169051E-05 6.4659119E-03 energy calculations done at 3.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 10:32:09 3.636u 0.172s 0:04.10 92.6% 0+0k 0+46184io 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 Jan 31 2012 at 10:32:09 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: 950 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3602 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: 1.687951 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): -2.179000 60.05100 ymin,ymax (A): -18.31500 44.95700 zmin,zma (A): -5.386000 54.96500 x,y,z range (A): 62.23000 63.27200 60.35100 scale (grids/A): 1.687951 object centre (A): 28.93600 13.32100 24.78950 number of atom coordinates read : 3602 total number of charged atoms : 3455 net assigned charge : -6.999962 assigned positive charge : 540.9139 centred at (gu) : 86.82170 78.80502 93.20196 assigned negative charge : -547.9156 centred at (gu) : 87.05853 78.62115 92.98840 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 81347 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32233 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 25989 mr = 55264 m= 2865 mr = 17762 m= 75 mr = 1350 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 35896 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 338 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 26664 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) : 0.5626502 object centre at (A) : 28.93600 13.32100 24.78950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.8468209E-03 2.7335372E-03 midg,1,midg; midg,igrid,midg -3.8037185E-02 2.0565984E-05 1,midg,midg; igrid,midg,midg -1.2696038E-02 -4.0628586E-02 gauss-seidel spectral radius is 0.9983590 estimated iterations to convergence 196 setup time was (sec) 0.8100000 now iterating at: 10:32:10 rms-change max change #iterations 3.970862 196.1417 at 10iterations 1.723559 66.16370 at 20iterations 0.7533376 23.48025 at 30iterations 0.3268753 11.50910 at 40iterations 0.1428974 4.678284 at 50iterations 6.2145479E-02 1.931176 at 60iterations 2.7133547E-02 0.8887634 at 70iterations 1.1852293E-02 0.4008589 at 80iterations 5.1920367E-03 0.1731606 at 90iterations 2.2933364E-03 7.6260567E-02 at 100iterations 1.0195157E-03 3.1539917E-02 at 110iterations 4.6642119E-04 1.6914368E-02 at 120iterations finished qdiffx linear iterations at : 10:32:18 total time elapsed so far: 8.050000 # loops : 120 mean,max change (kT/e) : 4.6642119E-04 1.6914368E-02 energy calculations done at 8.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.200000 DelPhi exited at 10:32:18 8.207u 0.224s 0:08.71 96.6% 0+0k 0+45408io 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 Jan 31 2012 at 10:32:18 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: 950 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3602 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: 2.531926 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): -2.179000 60.05100 ymin,ymax (A): -18.31500 44.95700 zmin,zma (A): -5.386000 54.96500 x,y,z range (A): 62.23000 63.27200 60.35100 scale (grids/A): 2.531926 object centre (A): 28.93600 13.32100 24.78950 number of atom coordinates read : 3602 total number of charged atoms : 3455 net assigned charge : -6.999962 assigned positive charge : 540.9139 centred at (gu) : 85.23220 73.20716 94.80251 assigned negative charge : -547.9156 centred at (gu) : 85.58756 72.93159 94.48245 start vw surface at 0.1200000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 188801 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32233 grid for indexing accessible points = 1.400000 m= 89135 mr = 135222 m= 26026 mr = 70257 m= 4448 mr = 19306 m= 349 mr = 2864 m= 7 mr = 115 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.580000 number of dielectric boundary points 81002 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 27619 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) : 1.687951 object centre at (A) : 28.93600 13.32100 24.78950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.1803473E-02 0.1959261 midg,1,midg; midg,igrid,midg -0.5378649 -4.0794769E-03 1,midg,midg; igrid,midg,midg -0.1801068 -0.7315218 gauss-seidel spectral radius is 0.9992059 estimated iterations to convergence 280 setup time was (sec) 1.810000 now iterating at: 10:32:20 rms-change max change #iterations 10.13642 311.4875 at 10iterations 5.822299 144.2413 at 20iterations 3.323513 69.90536 at 30iterations 1.897017 36.41497 at 40iterations 1.077095 20.14315 at 50iterations 0.6093815 12.94518 at 60iterations 0.3444227 6.493584 at 70iterations 0.1947698 3.552273 at 80iterations 0.1100076 1.862085 at 90iterations 6.2153261E-02 1.208679 at 100iterations 3.5056651E-02 0.6862965 at 110iterations 1.9788606E-02 0.3611603 at 120iterations 1.1155867E-02 0.2103701 at 130iterations 6.2950077E-03 0.1081674 at 140iterations 3.5670234E-03 6.6024780E-02 at 150iterations 2.0223074E-03 3.5194397E-02 at 160iterations 1.1580242E-03 2.1670818E-02 at 170iterations 6.6957402E-04 1.1880398E-02 at 180iterations finished qdiffx linear iterations at : 10:32:32 total time elapsed so far: 13.36000 # loops : 180 mean,max change (kT/e) : 6.6957402E-04 1.1880398E-02 energy calculations done at 13.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.50000 DelPhi exited at 10:32:32 13.504u 0.234s 0:14.04 97.7% 0+0k 0+45400io 0pf+0w