Sun Oct 9 08:19:49 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 Sun Oct 9 2011 at 08:19:50 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5929 !!! WARNING: HIR 702 has a net charge of 0.5140 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: 0.4800496 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): 3.856000 78.01500 ymin,ymax (A): 22.63900 85.72900 zmin,zma (A): 6.681000 70.72200 x,y,z range (A): 74.15900 63.09000 64.04100 scale (grids/A): 0.4800496 object centre (A): 40.93550 54.18400 38.70150 number of atom coordinates read : 5929 total number of charged atoms : 5761 net assigned charge : -0.4859560 assigned positive charge : 894.2869 centred at (gu) : 90.07202 88.73703 88.96284 assigned negative charge : -894.7808 centred at (gu) : 89.96194 88.73234 88.83881 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8405 nv = 96 ne = 84 npr = 119212 no. pairs analyzed = 119212 no. exposed pairs = 7494 no. arc points = 52261 no. surface atoms = 2511 nbur = 3418 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 = 1.792000 m= 258 mr = 4208 m= 0 mr = 2 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 4453 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4919 ## 870 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 11552 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3750975E-10 7.3234328E-11 midg,1,midg; midg,igrid,midg -5.9330900E-12 2.3804591E-12 1,midg,midg; igrid,midg,midg -8.8842309E-11 8.8959319E-11 gauss-seidel spectral radius is 0.9779028 estimated iterations to convergence 56 setup time was (sec) 0.7500000 now iterating at: 08:19:50 rms-change max change #iterations 5.4788299E-02 8.607506 at 10iterations 2.6304433E-03 0.3733358 at 20iterations 2.0470210E-04 3.9724350E-02 at 30iterations 4.4932891E-05 8.1539154E-03 at 40iterations 1.3179944E-05 1.9931793E-03 at 50iterations finished qdiffx linear iterations at : 08:19:53 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.3179944E-05 1.9931793E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 08:19:53 3.413u 0.147s 0:03.82 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 Sun Oct 9 2011 at 08:19:53 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5929 !!! WARNING: HIR 702 has a net charge of 0.5140 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: 1.440149 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): 3.856000 78.01500 ymin,ymax (A): 22.63900 85.72900 zmin,zma (A): 6.681000 70.72200 x,y,z range (A): 74.15900 63.09000 64.04100 scale (grids/A): 1.440149 object centre (A): 40.93550 54.18400 38.70150 number of atom coordinates read : 5929 total number of charged atoms : 5761 net assigned charge : -0.4859560 assigned positive charge : 894.2869 centred at (gu) : 90.21412 86.20943 86.88683 assigned negative charge : -894.7808 centred at (gu) : 89.88538 86.19671 86.51637 start vw surface at 0.2200000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 96931 reading accessible surface arcs data from file ARCDAT no. of arc points read = 52261 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 25205 mr = 65682 m= 1693 mr = 15743 m= 32 mr = 599 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 606 time to turn everything in is 0.6800000 number of dielectric boundary points 41837 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 937 ## 20 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 42296 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) : 0.4800496 object centre at (A) : 40.93550 54.18400 38.70150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.0369973E-03 1.1212591E-02 midg,1,midg; midg,igrid,midg -1.0850796E-03 -1.8145529E-03 1,midg,midg; igrid,midg,midg -5.9829424E-03 1.4182277E-02 gauss-seidel spectral radius is 0.9979370 estimated iterations to convergence 175 setup time was (sec) 0.9600000 now iterating at: 08:19:55 rms-change max change #iterations 3.721359 162.2750 at 10iterations 1.464530 61.39825 at 20iterations 0.5752521 16.83698 at 30iterations 0.2270355 7.248062 at 40iterations 8.9305021E-02 2.791371 at 50iterations 3.5339907E-02 1.057730 at 60iterations 1.3962639E-02 0.4266853 at 70iterations 5.5303257E-03 0.1646881 at 80iterations 2.2019930E-03 7.9887390E-02 at 90iterations 8.8631624E-04 2.7093887E-02 at 100iterations 3.6669831E-04 1.1959076E-02 at 110iterations 1.6190113E-04 5.5679083E-03 at 120iterations finished qdiffx linear iterations at : 08:20:01 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 1.6190113E-04 5.5679083E-03 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 08:20:02 7.745u 0.174s 0:08.19 96.5% 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 08:20:02 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5929 !!! WARNING: HIR 702 has a net charge of 0.5140 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: 2.160223 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): 3.856000 78.01500 ymin,ymax (A): 22.63900 85.72900 zmin,zma (A): 6.681000 70.72200 x,y,z range (A): 74.15900 63.09000 64.04100 scale (grids/A): 2.160223 object centre (A): 40.93550 54.18400 38.70150 number of atom coordinates read : 5929 total number of charged atoms : 5761 net assigned charge : -0.4859560 assigned positive charge : 894.2869 centred at (gu) : 90.32040 84.31377 85.32951 assigned negative charge : -894.7808 centred at (gu) : 89.82809 84.29487 84.77430 start vw surface at 0.2100000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 226778 reading accessible surface arcs data from file ARCDAT no. of arc points read = 52261 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 94170 mr = 162508 m= 19953 mr = 71565 m= 2080 mr = 13326 m= 66 mr = 1116 m= 0 mr = 11 time to grow re-entrant surface = 0.9299999 no. cavity mid-points inaccessible to solvent = 1974 time to turn everything in is 1.560000 number of dielectric boundary points 94521 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 164 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 45850 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) : 1.440149 object centre at (A) : 40.93550 54.18400 38.70150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1487503 0.2098372 midg,1,midg; midg,igrid,midg -1.3082280E-02 -3.3708319E-02 1,midg,midg; igrid,midg,midg 3.9926615E-02 0.2766674 gauss-seidel spectral radius is 0.9991372 estimated iterations to convergence 269 setup time was (sec) 1.880000 now iterating at: 08:20:04 rms-change max change #iterations 10.58595 322.5691 at 10iterations 6.059978 134.6334 at 20iterations 3.441248 83.93550 at 30iterations 1.939664 42.76929 at 40iterations 1.092983 26.45973 at 50iterations 0.6132261 13.50461 at 60iterations 0.3428454 6.996773 at 70iterations 0.1914017 3.955965 at 80iterations 0.1065690 1.993625 at 90iterations 5.9247367E-02 1.204213 at 100iterations 3.2934003E-02 0.6175308 at 110iterations 1.8250067E-02 0.3773317 at 120iterations 1.0121617E-02 0.2119827 at 130iterations 5.6100320E-03 0.1069489 at 140iterations 3.1086884E-03 6.0552597E-02 at 150iterations 1.7227569E-03 3.0506372E-02 at 160iterations 9.5672987E-04 1.7704010E-02 at 170iterations 5.3334719E-04 9.2406273E-03 at 180iterations finished qdiffx linear iterations at : 08:20:14 total time elapsed so far: 11.77000 # loops : 180 mean,max change (kT/e) : 5.3334719E-04 9.2406273E-03 energy calculations done at 11.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.95000 DelPhi exited at 08:20:14 11.950u 0.187s 0:12.42 97.6% 0+0k 0+0io 0pf+0w