Mon Oct 10 10:24:58 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 10:24:58 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2665 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: 0.5790030 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): 18.94200 80.42700 ymin,ymax (A): 33.71100 88.81300 zmin,zma (A): -1.291000 50.97700 x,y,z range (A): 61.48500 55.10201 52.26800 scale (grids/A): 0.5790030 object centre (A): 49.68450 61.26200 24.84300 number of atom coordinates read : 2665 total number of charged atoms : 2521 net assigned charge : 12.00002 assigned positive charge : 391.4871 centred at (gu) : 88.00690 88.51816 86.79839 assigned negative charge : -379.4876 centred at (gu) : 87.93626 88.52497 86.63545 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6101 nv = 96 ne = 84 npr = 50983 no. pairs analyzed = 50983 no. exposed pairs = 4005 no. arc points = 29164 no. surface atoms = 1325 nbur = 1340 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 = 1.484000 m= 283 mr = 2749 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.3100000 number of dielectric boundary points 3625 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2817 ## 317 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7630 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.4820785E-10 2.6232012E-09 midg,1,midg; midg,igrid,midg 3.8475463E-09 1.7872333E-09 1,midg,midg; igrid,midg,midg 2.0881148E-09 2.4493882E-09 gauss-seidel spectral radius is 0.9845958 estimated iterations to convergence 66 setup time was (sec) 0.6700000 now iterating at: 10:24:59 rms-change max change #iterations 9.0350412E-02 14.77248 at 10iterations 7.0506777E-03 1.197988 at 20iterations 5.3858280E-04 8.5960388E-02 at 30iterations 5.1281761E-05 8.7804794E-03 at 40iterations 7.2843836E-06 8.3923340E-04 at 50iterations finished qdiffx linear iterations at : 10:25:03 total time elapsed so far: 4.850000 # loops : 50 mean,max change (kT/e) : 7.2843836E-06 8.3923340E-04 energy calculations done at 4.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.010000 DelPhi exited at 10:25:03 5.015u 0.424s 0:05.80 93.6% 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 10:25:03 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2665 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: 1.737009 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): 18.94200 80.42700 ymin,ymax (A): 33.71100 88.81300 zmin,zma (A): -1.291000 50.97700 x,y,z range (A): 61.48500 55.10201 52.26800 scale (grids/A): 1.737009 object centre (A): 49.68450 61.26200 24.84300 number of atom coordinates read : 2665 total number of charged atoms : 2521 net assigned charge : 12.00002 assigned positive charge : 391.4871 centred at (gu) : 84.02027 85.55401 80.39484 assigned negative charge : -379.4876 centred at (gu) : 83.80854 85.57480 79.90616 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 65935 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29164 grid for indexing accessible points = 1.400000 m= 20170 mr = 40908 m= 2404 mr = 12733 m= 97 mr = 1076 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 33884 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 257 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 19523 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) : 0.5790030 object centre at (A) : 49.68450 61.26200 24.84300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6976901E-03 9.5339399E-03 midg,1,midg; midg,igrid,midg 2.4124306E-02 1.6345991E-02 1,midg,midg; igrid,midg,midg 2.9667472E-02 1.7812373E-02 gauss-seidel spectral radius is 0.9983823 estimated iterations to convergence 197 setup time was (sec) 0.9100000 now iterating at: 10:25:05 rms-change max change #iterations 3.484493 153.2110 at 10iterations 1.514939 60.85646 at 20iterations 0.6574523 24.78429 at 30iterations 0.2868963 10.43816 at 40iterations 0.1252289 4.697083 at 50iterations 5.4578263E-02 1.859730 at 60iterations 2.3836788E-02 0.9248468 at 70iterations 1.0404279E-02 0.3484698 at 80iterations 4.5392998E-03 0.1668825 at 90iterations 1.9801224E-03 7.0225954E-02 at 100iterations 8.6894922E-04 3.1208038E-02 at 110iterations 3.8027106E-04 1.4019012E-02 at 120iterations finished qdiffx linear iterations at : 10:25:16 total time elapsed so far: 11.90000 # loops : 120 mean,max change (kT/e) : 3.8027106E-04 1.4019012E-02 energy calculations done at 11.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.07000 DelPhi exited at 10:25:16 12.077u 0.480s 0:12.85 97.6% 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 10:25:16 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2665 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: 2.605514 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): 18.94200 80.42700 ymin,ymax (A): 33.71100 88.81300 zmin,zma (A): -1.291000 50.97700 x,y,z range (A): 61.48500 55.10201 52.26800 scale (grids/A): 2.605514 object centre (A): 49.68450 61.26200 24.84300 number of atom coordinates read : 2665 total number of charged atoms : 2521 net assigned charge : 12.00002 assigned positive charge : 391.4871 centred at (gu) : 81.03021 83.33099 75.59216 assigned negative charge : -379.4876 centred at (gu) : 80.71280 83.36218 74.85922 start vw surface at 0.1200000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 152480 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29164 grid for indexing accessible points = 1.400000 m= 67853 mr = 100865 m= 20547 mr = 50906 m= 3748 mr = 14471 m= 331 mr = 2171 m= 6 mr = 148 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.410000 number of dielectric boundary points 76404 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 20161 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) : 1.737009 object centre at (A) : 49.68450 61.26200 24.84300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9503039E-02 8.6916037E-02 midg,1,midg; midg,igrid,midg 0.2763059 0.2052446 1,midg,midg; igrid,midg,midg 0.4121861 0.4995454 gauss-seidel spectral radius is 0.9992006 estimated iterations to convergence 279 setup time was (sec) 1.770000 now iterating at: 10:25:19 rms-change max change #iterations 9.001216 283.3641 at 10iterations 5.295413 169.3551 at 20iterations 3.067297 83.67303 at 30iterations 1.767704 54.38392 at 40iterations 1.008474 26.39913 at 50iterations 0.5744910 14.35802 at 60iterations 0.3261364 8.102189 at 70iterations 0.1844962 4.384502 at 80iterations 0.1044263 2.508787 at 90iterations 5.9046760E-02 1.323834 at 100iterations 3.3219758E-02 0.7269077 at 110iterations 1.8754376E-02 0.4035072 at 120iterations 1.0527503E-02 0.2112045 at 130iterations 5.9276572E-03 0.1256065 at 140iterations 3.3365285E-03 7.8360558E-02 at 150iterations 1.8802739E-03 3.8757324E-02 at 160iterations 1.0555952E-03 2.1949768E-02 at 170iterations 5.9357268E-04 1.2001038E-02 at 180iterations finished qdiffx linear iterations at : 10:25:37 total time elapsed so far: 20.61000 # loops : 180 mean,max change (kT/e) : 5.9357268E-04 1.2001038E-02 energy calculations done at 20.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.78000 DelPhi exited at 10:25:38 20.785u 0.505s 0:21.58 98.6% 0+0k 0+0io 0pf+0w