Sun Oct 9 18:45:43 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 Sun Oct 9 2011 at 18:45:43 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 = 3277 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5221626 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): -8.194000 59.98400 ymin,ymax (A): -13.36300 35.07000 zmin,zma (A): 18.95800 69.75300 x,y,z range (A): 68.17800 48.43300 50.79500 scale (grids/A): 0.5221626 object centre (A): 25.89500 10.85350 44.35550 number of atom coordinates read : 3277 total number of charged atoms : 3130 net assigned charge : 11.00003 assigned positive charge : 502.3228 centred at (gu) : 90.87379 89.75137 89.32520 assigned negative charge : -491.3241 centred at (gu) : 90.85419 89.84519 89.28389 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5644 nv = 96 ne = 84 npr = 65517 no. pairs analyzed = 65517 no. exposed pairs = 4173 no. arc points = 29094 no. surface atoms = 1400 nbur = 1877 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= 230 mr = 2866 m= 0 mr = 5 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3003 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2862 ## 412 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7534 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6241240E-10 3.1776229E-10 midg,1,midg; midg,igrid,midg 5.6084143E-10 -1.4781851E-11 1,midg,midg; igrid,midg,midg 1.6238062E-10 3.9286477E-10 gauss-seidel spectral radius is 0.9811283 estimated iterations to convergence 60 setup time was (sec) 0.5500000 now iterating at: 18:45:44 rms-change max change #iterations 5.8667865E-02 8.599413 at 10iterations 3.6810855E-03 0.7751617 at 20iterations 4.0251427E-04 8.3627701E-02 at 30iterations 1.3853185E-04 2.3544312E-02 at 40iterations 6.9090296E-05 1.0758400E-02 at 50iterations finished qdiffx linear iterations at : 18:45:46 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 6.9090296E-05 1.0758400E-02 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 18:45:46 3.092u 0.152s 0:03.51 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 18:45:46 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3277 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: 1.566488 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): -8.194000 59.98400 ymin,ymax (A): -13.36300 35.07000 zmin,zma (A): 18.95800 69.75300 x,y,z range (A): 68.17800 48.43300 50.79500 scale (grids/A): 1.566488 object centre (A): 25.89500 10.85350 44.35550 number of atom coordinates read : 3277 total number of charged atoms : 3130 net assigned charge : 11.00003 assigned positive charge : 502.3228 centred at (gu) : 92.62064 89.25348 87.97476 assigned negative charge : -491.3241 centred at (gu) : 92.56217 89.53503 87.85130 start vw surface at 0.1700000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 63350 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29094 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 18547 mr = 42867 m= 1831 mr = 12086 m= 57 mr = 740 m= 0 mr = 4 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 28088 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 389 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 23640 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) : 0.5221626 object centre at (A) : 25.89500 10.85350 44.35550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.7155925E-03 5.7885624E-03 midg,1,midg; midg,igrid,midg 8.0464389E-03 -2.3239213E-03 1,midg,midg; igrid,midg,midg 1.7113032E-02 8.2165683E-03 gauss-seidel spectral radius is 0.9980421 estimated iterations to convergence 180 setup time was (sec) 0.7200000 now iterating at: 18:45:47 rms-change max change #iterations 3.205918 163.6171 at 10iterations 1.296304 49.10765 at 20iterations 0.5225847 19.93743 at 30iterations 0.2116506 8.605259 at 40iterations 8.5373081E-02 3.400577 at 50iterations 3.4645982E-02 1.362750 at 60iterations 1.4077990E-02 0.5681915 at 70iterations 5.7284804E-03 0.2592773 at 80iterations 2.3518761E-03 9.5886230E-02 at 90iterations 1.0022798E-03 3.8228989E-02 at 100iterations 4.6541030E-04 2.0404816E-02 at 110iterations 2.6292598E-04 9.8781586E-03 at 120iterations finished qdiffx linear iterations at : 18:45:53 total time elapsed so far: 6.570000 # loops : 120 mean,max change (kT/e) : 2.6292598E-04 9.8781586E-03 energy calculations done at 6.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.730000 DelPhi exited at 18:45:54 6.736u 0.160s 0:07.17 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 Sun Oct 9 2011 at 18:45:54 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 = 3277 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.349731 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): -8.194000 59.98400 ymin,ymax (A): -13.36300 35.07000 zmin,zma (A): 18.95800 69.75300 x,y,z range (A): 68.17800 48.43300 50.79500 scale (grids/A): 2.349731 object centre (A): 25.89500 10.85350 44.35550 number of atom coordinates read : 3277 total number of charged atoms : 3130 net assigned charge : 11.00003 assigned positive charge : 502.3228 centred at (gu) : 93.93065 88.88000 86.96203 assigned negative charge : -491.3241 centred at (gu) : 93.84321 89.30253 86.77695 start vw surface at 0.1700000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 147425 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29094 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 65625 mr = 105729 m= 17540 mr = 50288 m= 2570 mr = 12382 m= 161 mr = 1429 m= 2 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.060000 number of dielectric boundary points 63441 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 47 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 24984 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) : 1.566488 object centre at (A) : 25.89500 10.85350 44.35550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1876865 8.2135513E-02 midg,1,midg; midg,igrid,midg 0.1091532 -7.6174498E-02 1,midg,midg; igrid,midg,midg 0.6063510 -0.1175892 gauss-seidel spectral radius is 0.9990979 estimated iterations to convergence 263 setup time was (sec) 1.330000 now iterating at: 18:45:55 rms-change max change #iterations 8.583986 269.3962 at 10iterations 4.807739 147.8326 at 20iterations 2.670973 67.66143 at 30iterations 1.483106 39.32792 at 40iterations 0.8157415 19.33889 at 50iterations 0.4479073 13.41734 at 60iterations 0.2453467 5.962847 at 70iterations 0.1341622 3.580513 at 80iterations 7.3307797E-02 1.601460 at 90iterations 4.0021896E-02 0.9966621 at 100iterations 2.1827728E-02 0.5426364 at 110iterations 1.1889495E-02 0.2904568 at 120iterations 6.4775078E-03 0.1514435 at 130iterations 3.5168277E-03 7.9360008E-02 at 140iterations 1.9172626E-03 4.2170048E-02 at 150iterations 1.0437130E-03 2.5960684E-02 at 160iterations 5.6721154E-04 1.3656616E-02 at 170iterations 3.0798229E-04 7.0114136E-03 at 180iterations finished qdiffx linear iterations at : 18:46:04 total time elapsed so far: 10.48000 # loops : 180 mean,max change (kT/e) : 3.0798229E-04 7.0114136E-03 energy calculations done at 10.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.66000 DelPhi exited at 18:46:05 10.658u 0.155s 0:11.10 97.2% 0+0k 0+0io 0pf+0w