Wed Dec 28 11:01:24 PST 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 Wed Dec 28 2011 at 11:01:24 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6946478 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): 78.11200 129.3610 ymin,ymax (A): -8.000000 42.73000 zmin,zma (A): -2.576000 46.83400 x,y,z range (A): 51.24899 50.73000 49.41000 scale (grids/A): 0.6946478 object centre (A): 103.7365 17.36500 22.12900 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 4.000004 assigned positive charge : 288.5101 centred at (gu) : 87.52927 90.03996 92.01819 assigned negative charge : -284.5103 centred at (gu) : 87.40840 90.02433 92.18524 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6566 nv = 96 ne = 84 npr = 40067 no. pairs analyzed = 40067 no. exposed pairs = 2578 no. arc points = 17978 no. surface atoms = 875 nbur = 1085 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 430 mr = 3606 m= 2 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.3100000 number of dielectric boundary points 3309 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1733 ## 166 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7292 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.4929227E-08 -4.5720981E-08 midg,1,midg; midg,igrid,midg 2.1628049E-08 3.2449151E-08 1,midg,midg; igrid,midg,midg -2.4109644E-08 4.1191136E-08 gauss-seidel spectral radius is 0.9891971 estimated iterations to convergence 78 setup time was (sec) 0.6100000 now iterating at: 11:01:25 rms-change max change #iterations 0.1747235 28.08027 at 10iterations 2.0219142E-02 3.065088 at 20iterations 2.4424214E-03 0.3888168 at 30iterations 2.8766450E-04 4.0929794E-02 at 40iterations 3.3516946E-05 4.5127869E-03 at 50iterations finished qdiffx linear iterations at : 11:01:29 total time elapsed so far: 4.890000 # loops : 50 mean,max change (kT/e) : 3.3516946E-05 4.5127869E-03 energy calculations done at 4.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.090000 DelPhi exited at 11:01:30 5.095u 0.296s 0:05.69 94.5% 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 Dec 28 2011 at 11:01:30 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 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: 2.083943 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): 78.11200 129.3610 ymin,ymax (A): -8.000000 42.73000 zmin,zma (A): -2.576000 46.83400 x,y,z range (A): 51.24899 50.73000 49.41000 scale (grids/A): 2.083943 object centre (A): 103.7365 17.36500 22.12900 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 4.000004 assigned positive charge : 288.5101 centred at (gu) : 82.58768 90.11982 96.05431 assigned negative charge : -284.5103 centred at (gu) : 82.22546 90.07314 96.55575 start vw surface at 0.1400000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 69242 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17978 grid for indexing accessible points = 1.400000 m= 27148 mr = 47074 m= 5171 mr = 20907 m= 453 mr = 3630 m= 9 mr = 267 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 798 time to turn everything in is 0.6700000 number of dielectric boundary points 30145 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 73 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 14520 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) : 0.6946478 object centre at (A) : 103.7365 17.36500 22.12900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5433646E-02 -2.0033615E-02 midg,1,midg; midg,igrid,midg 8.0434456E-03 4.0213301E-04 1,midg,midg; igrid,midg,midg -6.7123966E-03 5.1863570E-02 gauss-seidel spectral radius is 0.9987783 estimated iterations to convergence 227 setup time was (sec) 1.040000 now iterating at: 11:01:31 rms-change max change #iterations 4.283502 186.6670 at 10iterations 2.085343 65.55245 at 20iterations 1.016515 34.07967 at 30iterations 0.4961928 15.40841 at 40iterations 0.2415779 7.475592 at 50iterations 0.1174095 3.986467 at 60iterations 5.7125621E-02 1.948383 at 70iterations 2.7925720E-02 0.9281356 at 80iterations 1.3593994E-02 0.4544830 at 90iterations 6.6339178E-03 0.2031407 at 100iterations 3.2328481E-03 9.8223209E-02 at 110iterations 1.5792755E-03 5.1681280E-02 at 120iterations finished qdiffx linear iterations at : 11:01:42 total time elapsed so far: 11.44000 # loops : 120 mean,max change (kT/e) : 1.5792755E-03 5.1681280E-02 energy calculations done at 11.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.63000 DelPhi exited at 11:01:42 11.631u 0.566s 0:12.77 95.4% 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 Wed Dec 28 2011 at 11:01:42 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.125915 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): 78.11200 129.3610 ymin,ymax (A): -8.000000 42.73000 zmin,zma (A): -2.576000 46.83400 x,y,z range (A): 51.24899 50.73000 49.41000 scale (grids/A): 3.125915 object centre (A): 103.7365 17.36500 22.12900 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 4.000004 assigned positive charge : 288.5101 centred at (gu) : 78.88148 90.17995 99.08134 assigned negative charge : -284.5103 centred at (gu) : 78.33830 90.10973 99.83379 start vw surface at 0.1500000 fill in re-entrant regions at 0.9300000 boundary points on vw surface= 159338 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17978 grid for indexing accessible points = 1.400000 m= 84094 mr = 113594 m= 34591 mr = 69896 m= 9736 mr = 29003 m= 2061 mr = 7931 m= 241 mr = 1664 m= 8 mr = 161 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 2469 time to turn everything in is 2.130000 number of dielectric boundary points 67820 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.320000 number of grid points assigned charge 14624 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) : 2.083943 object centre at (A) : 103.7365 17.36500 22.12900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5271178 -0.2799825 midg,1,midg; midg,igrid,midg -4.0390063E-02 -7.7761360E-02 1,midg,midg; igrid,midg,midg -0.1038916 0.4405250 gauss-seidel spectral radius is 0.9992965 estimated iterations to convergence 297 setup time was (sec) 2.560000 now iterating at: 11:01:45 rms-change max change #iterations 9.730539 507.2789 at 10iterations 5.670786 143.9632 at 20iterations 3.349035 76.48301 at 30iterations 1.957777 41.16208 at 40iterations 1.141892 25.64185 at 50iterations 0.6652237 14.76751 at 60iterations 0.3881633 7.340460 at 70iterations 0.2256155 3.933226 at 80iterations 0.1315520 2.474557 at 90iterations 7.6382793E-02 1.513258 at 100iterations 4.4442352E-02 0.7662659 at 110iterations 2.5845710E-02 0.5199623 at 120iterations 1.5081022E-02 0.3028238 at 130iterations 8.7515479E-03 0.1527965 at 140iterations 5.0878790E-03 9.4528198E-02 at 150iterations 2.9638987E-03 5.5911541E-02 at 160iterations 1.7236581E-03 3.2368779E-02 at 170iterations 1.0044283E-03 1.8157959E-02 at 180iterations finished qdiffx linear iterations at : 11:02:04 total time elapsed so far: 20.64000 # loops : 180 mean,max change (kT/e) : 1.0044283E-03 1.8157959E-02 energy calculations done at 20.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.81000 DelPhi exited at 11:02:06 20.812u 0.567s 0:23.36 91.4% 0+0k 0+0io 0pf+0w