Sun Oct 9 08:19:45 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 08:19:45 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 = 6120 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: 0.4697933 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): -30.34900 34.18900 ymin,ymax (A): -33.14800 31.13400 zmin,zma (A): -32.75400 43.02400 x,y,z range (A): 64.53800 64.28200 75.77800 scale (grids/A): 0.4697933 object centre (A): 1.920002 -1.007000 5.135000 number of atom coordinates read : 6120 total number of charged atoms : 5950 net assigned charge : -1.999962 assigned positive charge : 920.9466 centred at (gu) : 90.91840 90.01322 90.04639 assigned negative charge : -922.9547 centred at (gu) : 90.86292 90.03868 89.92824 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8185 nv = 96 ne = 84 npr = 124468 no. pairs analyzed = 124468 no. exposed pairs = 7601 no. arc points = 52546 no. surface atoms = 2552 nbur = 3568 mkacc time = 0.2200000 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 = 1.820000 m= 262 mr = 4124 m= 0 mr = 2 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.3900000 number of dielectric boundary points 4321 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4858 ## 868 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 11283 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.3891947E-11 5.5016321E-11 midg,1,midg; midg,igrid,midg 8.5226314E-12 -1.7152496E-11 1,midg,midg; igrid,midg,midg -2.4904854E-11 3.0738637E-11 gauss-seidel spectral radius is 0.9769413 estimated iterations to convergence 55 setup time was (sec) 0.6100000 now iterating at: 08:19:45 rms-change max change #iterations 4.9878668E-02 10.36285 at 10iterations 2.5115639E-03 0.4598312 at 20iterations 2.3522812E-04 4.8307419E-02 at 30iterations 4.6169345E-05 9.2239380E-03 at 40iterations 1.2088049E-05 2.0027161E-03 at 50iterations finished qdiffx linear iterations at : 08:19:49 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 1.2088049E-05 2.0027161E-03 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.090000 DelPhi exited at 08:19:49 4.094u 0.241s 0:04.89 88.5% 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 Sun Oct 9 2011 at 08:19:49 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 = 6120 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: 1.409380 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): -30.34900 34.18900 ymin,ymax (A): -33.14800 31.13400 zmin,zma (A): -32.75400 43.02400 x,y,z range (A): 64.53800 64.28200 75.77800 scale (grids/A): 1.409380 object centre (A): 1.920002 -1.007000 5.135000 number of atom coordinates read : 6120 total number of charged atoms : 5950 net assigned charge : -1.999962 assigned positive charge : 920.9466 centred at (gu) : 92.75349 90.03743 90.13737 assigned negative charge : -922.9547 centred at (gu) : 92.58842 90.11569 89.78448 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 94891 reading accessible surface arcs data from file ARCDAT no. of arc points read = 52546 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.708000 m= 24093 mr = 64479 m= 1508 mr = 15053 m= 14 mr = 463 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 471 time to turn everything in is 0.4800000 number of dielectric boundary points 40511 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 912 ## 23 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 43267 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) : 0.4697933 object centre at (A) : 1.920002 -1.007000 5.135000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8109992E-02 8.3423154E-03 midg,1,midg; midg,igrid,midg -6.4472973E-05 -1.1373218E-03 1,midg,midg; igrid,midg,midg -6.8909116E-03 3.9869262E-04 gauss-seidel spectral radius is 0.9978464 estimated iterations to convergence 171 setup time was (sec) 0.7300000 now iterating at: 08:19:50 rms-change max change #iterations 3.592868 160.4652 at 10iterations 1.384337 44.91406 at 20iterations 0.5351315 17.68103 at 30iterations 0.2072516 6.871590 at 40iterations 7.9968087E-02 2.612003 at 50iterations 3.1017832E-02 1.001564 at 60iterations 1.1996890E-02 0.3832092 at 70iterations 4.6856911E-03 0.1607857 at 80iterations 1.8464888E-03 6.0150146E-02 at 90iterations 7.4244215E-04 2.4917603E-02 at 100iterations 3.1323548E-04 9.8896027E-03 at 110iterations 1.4677817E-04 5.5313110E-03 at 120iterations finished qdiffx linear iterations at : 08:19:58 total time elapsed so far: 8.530000 # loops : 120 mean,max change (kT/e) : 1.4677817E-04 5.5313110E-03 energy calculations done at 8.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.660000 DelPhi exited at 08:19:59 8.665u 0.234s 0:09.17 96.9% 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 Sun Oct 9 2011 at 08:19:59 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 = 6120 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: 2.114070 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): -30.34900 34.18900 ymin,ymax (A): -33.14800 31.13400 zmin,zma (A): -32.75400 43.02400 x,y,z range (A): 64.53800 64.28200 75.77800 scale (grids/A): 2.114070 object centre (A): 1.920002 -1.007000 5.135000 number of atom coordinates read : 6120 total number of charged atoms : 5950 net assigned charge : -1.999962 assigned positive charge : 920.9466 centred at (gu) : 94.12979 90.05588 90.20543 assigned negative charge : -922.9547 centred at (gu) : 93.88267 90.17358 89.67675 start vw surface at 0.1400000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 222026 reading accessible surface arcs data from file ARCDAT no. of arc points read = 52546 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 91397 mr = 159587 m= 18790 mr = 69228 m= 1767 mr = 12682 m= 42 mr = 893 m= 0 mr = 2 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 1808 time to turn everything in is 1.150000 number of dielectric boundary points 91630 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 170 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 47260 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) : 1.409380 object centre at (A) : 1.920002 -1.007000 5.135000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6131397 -2.7388128E-02 midg,1,midg; midg,igrid,midg 7.4243410E-03 -6.6664172E-03 1,midg,midg; igrid,midg,midg -0.1612345 -2.0074097E-02 gauss-seidel spectral radius is 0.9991170 estimated iterations to convergence 266 setup time was (sec) 1.430000 now iterating at: 08:20:00 rms-change max change #iterations 10.37198 295.8065 at 10iterations 5.913158 137.3116 at 20iterations 3.343035 78.31573 at 30iterations 1.877906 53.34848 at 40iterations 1.054060 24.46814 at 50iterations 0.5876370 14.94823 at 60iterations 0.3269927 7.096885 at 70iterations 0.1815157 3.708065 at 80iterations 0.1005127 2.299161 at 90iterations 5.5619143E-02 1.070915 at 100iterations 3.0680975E-02 0.6439571 at 110iterations 1.6955540E-02 0.3267536 at 120iterations 9.3485778E-03 0.2035446 at 130iterations 5.1492825E-03 0.1028347 at 140iterations 2.8396421E-03 5.7963371E-02 at 150iterations 1.5705221E-03 2.8678894E-02 at 160iterations 8.6650491E-04 1.6485214E-02 at 170iterations 4.8146286E-04 9.0050697E-03 at 180iterations finished qdiffx linear iterations at : 08:20:13 total time elapsed so far: 14.41000 # loops : 180 mean,max change (kT/e) : 4.8146286E-04 9.0050697E-03 energy calculations done at 14.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.54000 DelPhi exited at 08:20:14 14.541u 0.278s 0:15.11 98.0% 0+0k 0+0io 0pf+0w