Mon Oct 10 14:07:52 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 Mon Oct 10 2011 at 14:07:52 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5882 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.4856687 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): 14.81000 80.48500 ymin,ymax (A): 18.45400 85.09000 zmin,zma (A): -5.157000 68.14400 x,y,z range (A): 65.67500 66.63600 73.30099 scale (grids/A): 0.4856687 object centre (A): 47.64750 51.77200 31.49350 number of atom coordinates read : 5882 total number of charged atoms : 5714 net assigned charge : 0.5000445 assigned positive charge : 884.6201 centred at (gu) : 90.07538 89.42319 90.68340 assigned negative charge : -884.1278 centred at (gu) : 90.02119 89.44057 90.82465 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8733 nv = 96 ne = 84 npr = 117079 no. pairs analyzed = 117079 no. exposed pairs = 7600 no. arc points = 52582 no. surface atoms = 2554 nbur = 3328 mkacc time = 0.2500000 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 = 1.764000 m= 284 mr = 4376 m= 2 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 4641 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4975 ## 841 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 11786 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2257294E-10 -1.7893878E-10 midg,1,midg; midg,igrid,midg 2.5187458E-11 -1.2724779E-11 1,midg,midg; igrid,midg,midg -5.2760567E-11 6.0854009E-11 gauss-seidel spectral radius is 0.9784112 estimated iterations to convergence 56 setup time was (sec) 0.7600000 now iterating at: 14:07:53 rms-change max change #iterations 5.6067575E-02 9.521248 at 10iterations 3.1698556E-03 0.4776840 at 20iterations 4.2477090E-04 0.1026764 at 30iterations 1.1453593E-04 2.7261734E-02 at 40iterations 3.5679492E-05 7.8907013E-03 at 50iterations finished qdiffx linear iterations at : 14:07:56 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 3.5679492E-05 7.8907013E-03 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 14:07:57 3.534u 0.188s 0:04.12 90.0% 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 Mon Oct 10 2011 at 14:07:57 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5882 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.457006 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): 14.81000 80.48500 ymin,ymax (A): 18.45400 85.09000 zmin,zma (A): -5.157000 68.14400 x,y,z range (A): 65.67500 66.63600 73.30099 scale (grids/A): 1.457006 object centre (A): 47.64750 51.77200 31.49350 number of atom coordinates read : 5882 total number of charged atoms : 5714 net assigned charge : 0.5000445 assigned positive charge : 884.6201 centred at (gu) : 90.22471 88.26779 92.04900 assigned negative charge : -884.1278 centred at (gu) : 90.06329 88.32199 92.47345 start vw surface at 0.2100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 99179 reading accessible surface arcs data from file ARCDAT no. of arc points read = 52582 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 27927 mr = 66988 m= 1999 mr = 17760 m= 32 mr = 594 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 277 time to turn everything in is 0.7100000 number of dielectric boundary points 43795 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 830 ## 13 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 42011 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) : 0.4856687 object centre at (A) : 47.64750 51.77200 31.49350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9012593E-02 -3.5286054E-02 midg,1,midg; midg,igrid,midg 3.6810848E-04 -7.7401148E-03 1,midg,midg; igrid,midg,midg 1.2754928E-03 7.5312071E-03 gauss-seidel spectral radius is 0.9979994 estimated iterations to convergence 178 setup time was (sec) 1.000000 now iterating at: 14:07:58 rms-change max change #iterations 3.809187 188.5000 at 10iterations 1.519053 48.39590 at 20iterations 0.6065236 19.02443 at 30iterations 0.2436831 7.734063 at 40iterations 9.7254649E-02 2.900927 at 50iterations 3.9008185E-02 1.346634 at 60iterations 1.5664747E-02 0.4901323 at 70iterations 6.3025611E-03 0.2049255 at 80iterations 2.5786168E-03 8.5903168E-02 at 90iterations 1.0801881E-03 3.5701752E-02 at 100iterations 4.8291520E-04 2.0801544E-02 at 110iterations 2.3684018E-04 1.0509491E-02 at 120iterations finished qdiffx linear iterations at : 14:08:04 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 2.3684018E-04 1.0509491E-02 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 14:08:05 7.688u 0.233s 0:08.51 92.9% 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 Mon Oct 10 2011 at 14:08:05 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 # of charge parameter records: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5882 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.185509 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): 14.81000 80.48500 ymin,ymax (A): 18.45400 85.09000 zmin,zma (A): -5.157000 68.14400 x,y,z range (A): 65.67500 66.63600 73.30099 scale (grids/A): 2.185509 object centre (A): 47.64750 51.77200 31.49350 number of atom coordinates read : 5882 total number of charged atoms : 5714 net assigned charge : 0.5000445 assigned positive charge : 884.6201 centred at (gu) : 90.33646 87.40159 93.07291 assigned negative charge : -884.1278 centred at (gu) : 90.09489 87.48283 93.71022 start vw surface at 0.2000000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 231217 reading accessible surface arcs data from file ARCDAT no. of arc points read = 52582 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 101595 mr = 165367 m= 23444 mr = 77540 m= 2571 mr = 15938 m= 75 mr = 1229 m= 0 mr = 3 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 975 time to turn everything in is 1.650000 number of dielectric boundary points 98825 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 138 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 45479 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) : 1.457006 object centre at (A) : 47.64750 51.77200 31.49350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4939084 -0.9432270 midg,1,midg; midg,igrid,midg 1.2219793E-02 -0.1647695 1,midg,midg; igrid,midg,midg 5.7116639E-02 9.0400144E-02 gauss-seidel spectral radius is 0.9991651 estimated iterations to convergence 273 setup time was (sec) 1.970000 now iterating at: 14:08:07 rms-change max change #iterations 10.87018 352.8580 at 10iterations 6.281539 151.1019 at 20iterations 3.608932 81.79756 at 30iterations 2.062831 46.50328 at 40iterations 1.174032 24.85065 at 50iterations 0.6663414 17.25439 at 60iterations 0.3752325 9.710913 at 70iterations 0.2117677 4.013182 at 80iterations 0.1189973 2.440384 at 90iterations 6.6941991E-02 1.356479 at 100iterations 3.7493341E-02 0.7094164 at 110iterations 2.1007545E-02 0.3815861 at 120iterations 1.1756032E-02 0.2136455 at 130iterations 6.5889335E-03 0.1345520 at 140iterations 3.6891461E-03 6.8814516E-02 at 150iterations 2.0641352E-03 3.7698746E-02 at 160iterations 1.1586525E-03 2.0246506E-02 at 170iterations 6.5149728E-04 1.1716485E-02 at 180iterations finished qdiffx linear iterations at : 14:08:18 total time elapsed so far: 12.60000 # loops : 180 mean,max change (kT/e) : 6.5149728E-04 1.1716485E-02 energy calculations done at 12.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.81000 DelPhi exited at 14:08:19 12.817u 0.224s 0:13.68 95.2% 0+0k 0+0io 0pf+0w