Sat Oct 8 18:10:39 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 Sat Oct 8 2011 at 18:10:39 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 = 3411 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: 0.5751955 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): -1.853000 53.66100 ymin,ymax (A): -18.46100 39.04700 zmin,zma (A): -6.505000 55.38700 x,y,z range (A): 55.51400 57.50800 61.89200 scale (grids/A): 0.5751955 object centre (A): 25.90400 10.29300 24.44100 number of atom coordinates read : 3411 total number of charged atoms : 3265 net assigned charge : -5.999965 assigned positive charge : 507.8516 centred at (gu) : 89.92980 87.49158 90.91895 assigned negative charge : -513.8528 centred at (gu) : 89.97991 87.48796 90.91876 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7400 nv = 96 ne = 84 npr = 69349 no. pairs analyzed = 69349 no. exposed pairs = 4412 no. arc points = 31187 no. surface atoms = 1478 nbur = 1933 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= 339 mr = 3869 m= 0 mr = 14 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3856 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3054 ## 329 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9515 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.9369878E-10 -1.3497329E-09 midg,1,midg; midg,igrid,midg -2.1062805E-09 -5.8079086E-10 1,midg,midg; igrid,midg,midg -2.6423719E-11 -2.1447528E-09 gauss-seidel spectral radius is 0.9844376 estimated iterations to convergence 66 setup time was (sec) 0.5600000 now iterating at: 18:10:40 rms-change max change #iterations 9.8318718E-02 15.70729 at 10iterations 7.6995362E-03 1.043286 at 20iterations 6.4110133E-04 0.1166964 at 30iterations 8.6738895E-05 1.6431808E-02 at 40iterations 2.2808534E-05 4.5166016E-03 at 50iterations finished qdiffx linear iterations at : 18:10:43 total time elapsed so far: 3.020000 # loops : 50 mean,max change (kT/e) : 2.2808534E-05 4.5166016E-03 energy calculations done at 3.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.190000 DelPhi exited at 18:10:43 3.197u 0.182s 0:03.68 91.5% 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 Sat Oct 8 2011 at 18:10:43 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 = 3411 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.725587 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): -1.853000 53.66100 ymin,ymax (A): -18.46100 39.04700 zmin,zma (A): -6.505000 55.38700 x,y,z range (A): 55.51400 57.50800 61.89200 scale (grids/A): 1.725587 object centre (A): 25.90400 10.29300 24.44100 number of atom coordinates read : 3411 total number of charged atoms : 3265 net assigned charge : -5.999965 assigned positive charge : 507.8516 centred at (gu) : 89.78852 82.47365 92.75613 assigned negative charge : -513.8528 centred at (gu) : 89.93902 82.46349 92.75585 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 81432 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31187 grid for indexing accessible points = 1.400000 m= 26855 mr = 55570 m= 3126 mr = 18538 m= 98 mr = 1548 m= 2 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 224 time to turn everything in is 0.5500000 number of dielectric boundary points 35850 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 284 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 25292 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) : 0.5751955 object centre at (A) : 25.90400 10.29300 24.44100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0267835E-03 -9.0311207E-03 midg,1,midg; midg,igrid,midg -2.6860518E-02 -1.5767049E-03 1,midg,midg; igrid,midg,midg -8.2978373E-03 -4.3840952E-02 gauss-seidel spectral radius is 0.9984252 estimated iterations to convergence 200 setup time was (sec) 0.8400000 now iterating at: 18:10:44 rms-change max change #iterations 4.024863 165.2199 at 10iterations 1.770450 60.68386 at 20iterations 0.7818353 26.39664 at 30iterations 0.3470401 12.29850 at 40iterations 0.1534052 5.376921 at 50iterations 6.7913517E-02 2.213922 at 60iterations 3.0070011E-02 1.021600 at 70iterations 1.3303752E-02 0.4263382 at 80iterations 5.9283748E-03 0.1940536 at 90iterations 2.6329325E-03 8.0275536E-02 at 100iterations 1.1798388E-03 3.6738873E-02 at 110iterations 5.2912248E-04 1.6592503E-02 at 120iterations finished qdiffx linear iterations at : 18:10:50 total time elapsed so far: 6.910000 # loops : 120 mean,max change (kT/e) : 5.2912248E-04 1.6592503E-02 energy calculations done at 6.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.090000 DelPhi exited at 18:10:51 7.089u 0.201s 0:07.56 96.2% 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 Sat Oct 8 2011 at 18:10:51 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 = 3411 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: 2.588380 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): -1.853000 53.66100 ymin,ymax (A): -18.46100 39.04700 zmin,zma (A): -6.505000 55.38700 x,y,z range (A): 55.51400 57.50800 61.89200 scale (grids/A): 2.588380 object centre (A): 25.90400 10.29300 24.44100 number of atom coordinates read : 3411 total number of charged atoms : 3265 net assigned charge : -5.999965 assigned positive charge : 507.8516 centred at (gu) : 89.68271 78.71030 94.13396 assigned negative charge : -513.8528 centred at (gu) : 89.90851 78.69505 94.13374 start vw surface at 0.1700000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 188858 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31187 grid for indexing accessible points = 1.400000 m= 90615 mr = 135568 m= 27711 mr = 71974 m= 4932 mr = 20745 m= 411 mr = 3213 m= 15 mr = 180 m= 0 mr = 2 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 887 time to turn everything in is 1.380000 number of dielectric boundary points 80860 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 26100 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) : 1.725587 object centre at (A) : 25.90400 10.29300 24.44100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0577796E-02 3.4044441E-02 midg,1,midg; midg,igrid,midg -0.3751784 -4.6522222E-03 1,midg,midg; igrid,midg,midg -0.1426688 -0.7747193 gauss-seidel spectral radius is 0.9992230 estimated iterations to convergence 283 setup time was (sec) 1.680000 now iterating at: 18:10:53 rms-change max change #iterations 10.10153 296.1854 at 10iterations 5.869670 138.9930 at 20iterations 3.386136 66.06671 at 30iterations 1.945407 40.08768 at 40iterations 1.116535 20.59620 at 50iterations 0.6370024 11.85836 at 60iterations 0.3634179 6.891603 at 70iterations 0.2067318 4.081103 at 80iterations 0.1175577 2.333552 at 90iterations 6.6905193E-02 1.266016 at 100iterations 3.8003020E-02 0.6747770 at 110iterations 2.1559574E-02 0.4673157 at 120iterations 1.2243726E-02 0.2174854 at 130iterations 6.9389688E-03 0.1360936 at 140iterations 3.9471737E-03 7.3480606E-02 at 150iterations 2.2455249E-03 3.9875984E-02 at 160iterations 1.2787880E-03 2.3830414E-02 at 170iterations 7.3465559E-04 1.3336182E-02 at 180iterations finished qdiffx linear iterations at : 18:11:02 total time elapsed so far: 11.37000 # loops : 180 mean,max change (kT/e) : 7.3465559E-04 1.3336182E-02 energy calculations done at 11.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.54000 DelPhi exited at 18:11:03 11.547u 0.218s 0:12.04 97.5% 0+0k 0+0io 0pf+0w