Wed Dec 21 14:21:11 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+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 Wed Dec 21 2011 at 14:21:11 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 = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5941751 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): -35.17700 11.30000 ymin,ymax (A): 0.9910001 41.33600 zmin,zma (A): -1.194000 58.72100 x,y,z range (A): 46.47700 40.34500 59.91500 scale (grids/A): 0.5941751 object centre (A): -11.93850 21.16350 28.76350 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000007 assigned positive charge : 293.7999 centred at (gu) : 90.14345 89.50050 89.44587 assigned negative charge : -291.8002 centred at (gu) : 90.02847 89.66103 89.44597 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 4737 nv = 96 ne = 84 npr = 40133 no. pairs analyzed = 40133 no. exposed pairs = 2434 no. arc points = 17041 no. surface atoms = 837 nbur = 1133 mkacc time = 6.9999993E-02 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 = 1.484000 m= 199 mr = 2581 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 2346 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1777 ## 202 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 5801 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.8003448E-10 6.0638000E-10 midg,1,midg; midg,igrid,midg 4.8186597E-09 -2.7150220E-09 1,midg,midg; igrid,midg,midg -1.9117885E-09 3.3930405E-09 gauss-seidel spectral radius is 0.9852908 estimated iterations to convergence 68 setup time was (sec) 0.4900000 now iterating at: 14:21:12 rms-change max change #iterations 9.1665909E-02 15.78581 at 10iterations 7.4812500E-03 1.266863 at 20iterations 6.2871043E-04 0.1084919 at 30iterations 5.0606279E-05 7.9078674E-03 at 40iterations 4.1813223E-06 8.8500977E-04 at 50iterations finished qdiffx linear iterations at : 14:21:16 total time elapsed so far: 4.550000 # loops : 50 mean,max change (kT/e) : 4.1813223E-06 8.8500977E-04 energy calculations done at 4.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.680000 DelPhi exited at 14:21:19 4.684u 0.391s 0:09.15 55.4% 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 21 2011 at 14:21:22 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 = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.782525 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): -35.17700 11.30000 ymin,ymax (A): 0.9910001 41.33600 zmin,zma (A): -1.194000 58.72100 x,y,z range (A): 46.47700 40.34500 59.91500 scale (grids/A): 1.782525 object centre (A): -11.93850 21.16350 28.76350 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000007 assigned positive charge : 293.7999 centred at (gu) : 90.43027 88.50153 88.33728 assigned negative charge : -291.8002 centred at (gu) : 90.08537 88.98326 88.33815 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 51358 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17041 grid for indexing accessible points = 1.400000 m= 17881 mr = 35293 m= 2252 mr = 13310 m= 98 mr = 1316 m= 0 mr = 8 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 21662 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 186 iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 14342 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) : 0.5941751 object centre at (A) : -11.93850 21.16350 28.76350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2723309E-02 2.5632404E-02 midg,1,midg; midg,igrid,midg 1.3004938E-03 -9.8469937E-03 1,midg,midg; igrid,midg,midg -4.3356037E-03 7.4268255E-04 gauss-seidel spectral radius is 0.9983675 estimated iterations to convergence 196 setup time was (sec) 0.4900000 now iterating at: 14:21:24 rms-change max change #iterations 3.223153 159.6073 at 10iterations 1.405752 53.74261 at 20iterations 0.6156871 26.95735 at 30iterations 0.2679019 11.28994 at 40iterations 0.1162410 4.456809 at 50iterations 5.0813124E-02 2.178104 at 60iterations 2.2160457E-02 0.8493519 at 70iterations 9.6889967E-03 0.3889389 at 80iterations 4.2208093E-03 0.1786671 at 90iterations 1.8364507E-03 7.0941925E-02 at 100iterations 8.0148183E-04 3.3403397E-02 at 110iterations 3.5125023E-04 1.3223648E-02 at 120iterations finished qdiffx linear iterations at : 14:21:32 total time elapsed so far: 8.810000 # loops : 120 mean,max change (kT/e) : 3.5125023E-04 1.3223648E-02 energy calculations done at 8.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.950000 DelPhi exited at 14:21:44 8.957u 0.210s 0:22.19 41.2% 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 21 2011 at 14:21:44 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 = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.673788 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): -35.17700 11.30000 ymin,ymax (A): 0.9910001 41.33600 zmin,zma (A): -1.194000 58.72100 x,y,z range (A): 46.47700 40.34500 59.91500 scale (grids/A): 2.673788 object centre (A): -11.93850 21.16350 28.76350 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000007 assigned positive charge : 293.7999 centred at (gu) : 90.64519 87.75220 87.50582 assigned negative charge : -291.8002 centred at (gu) : 90.12806 88.47484 87.50730 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 118689 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17041 grid for indexing accessible points = 1.400000 m= 58878 mr = 85352 m= 19863 mr = 48387 m= 3891 mr = 16194 m= 390 mr = 2721 m= 6 mr = 221 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7500000 number of dielectric boundary points 48842 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 14701 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) : 1.782525 object centre at (A) : -11.93850 21.16350 28.76350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4271611E-02 0.2641724 midg,1,midg; midg,igrid,midg -2.9267414E-02 -0.1350006 1,midg,midg; igrid,midg,midg -7.5387150E-02 -3.0950269E-02 gauss-seidel spectral radius is 0.9991611 estimated iterations to convergence 273 setup time was (sec) 1.170000 now iterating at: 14:21:46 rms-change max change #iterations 7.785347 346.9120 at 10iterations 4.358787 139.2444 at 20iterations 2.430691 95.97649 at 30iterations 1.351247 60.43051 at 40iterations 0.7474993 17.89219 at 50iterations 0.4141865 9.349907 at 60iterations 0.2286873 5.015238 at 70iterations 0.1265417 2.696936 at 80iterations 6.9815591E-02 1.552537 at 90iterations 3.8621068E-02 0.8501358 at 100iterations 2.1425525E-02 0.4851632 at 110iterations 1.1856607E-02 0.2577419 at 120iterations 6.5471027E-03 0.1507006 at 130iterations 3.6172403E-03 7.7968597E-02 at 140iterations 1.9994238E-03 4.4364929E-02 at 150iterations 1.1013557E-03 2.3952961E-02 at 160iterations 6.0984970E-04 1.3197422E-02 at 170iterations 3.3765068E-04 9.0179443E-03 at 180iterations finished qdiffx linear iterations at : 14:22:00 total time elapsed so far: 15.20000 # loops : 180 mean,max change (kT/e) : 3.3765068E-04 9.0179443E-03 energy calculations done at 15.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.33000 DelPhi exited at 14:22:16 15.333u 0.408s 0:32.15 48.9% 0+0k 0+0io 0pf+0w