Sun Oct 9 14:36:45 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+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 14:36:45 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2703 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: SEP 329 has a net charge of -0.4750 !!! WARNING: GLM 356 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5543099 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): 0.1330000 50.63400 ymin,ymax (A): -9.988999 39.96200 zmin,zma (A): -17.41400 46.81000 x,y,z range (A): 50.50100 49.95100 64.22400 scale (grids/A): 0.5543099 object centre (A): 25.38350 14.98650 14.69800 number of atom coordinates read : 2703 total number of charged atoms : 2556 net assigned charge : 5.445022 assigned positive charge : 411.5585 centred at (gu) : 90.06305 90.46225 89.09232 assigned negative charge : -406.1145 centred at (gu) : 90.06451 90.37576 89.16509 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5437 nv = 96 ne = 84 npr = 53258 no. pairs analyzed = 53258 no. exposed pairs = 3459 no. arc points = 24594 no. surface atoms = 1164 nbur = 1539 mkacc time = 0.1300000 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 = 1.540000 m= 221 mr = 2726 m= 0 mr = 5 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 2927 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2595 ## 328 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7107 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3145398E-09 -1.1415607E-10 midg,1,midg; midg,igrid,midg -2.3253557E-10 1.3030080E-09 1,midg,midg; igrid,midg,midg 4.6306348E-10 4.5252960E-10 gauss-seidel spectral radius is 0.9831957 estimated iterations to convergence 63 setup time was (sec) 0.5400000 now iterating at: 14:36:45 rms-change max change #iterations 7.5072832E-02 13.77131 at 10iterations 5.3137736E-03 0.9893532 at 20iterations 3.8841390E-04 7.3462009E-02 at 30iterations 3.7287766E-05 5.8691502E-03 at 40iterations 5.9121744E-06 9.8299980E-04 at 50iterations finished qdiffx linear iterations at : 14:36:48 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 5.9121744E-06 9.8299980E-04 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 14:36:49 3.361u 0.151s 0:03.79 92.6% 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 Sun Oct 9 2011 at 14:36:49 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2703 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: SEP 329 has a net charge of -0.4750 !!! WARNING: GLM 356 has a net charge of -0.0940 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: 1.662930 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): 0.1330000 50.63400 ymin,ymax (A): -9.988999 39.96200 zmin,zma (A): -17.41400 46.81000 x,y,z range (A): 50.50100 49.95100 64.22400 scale (grids/A): 1.662930 object centre (A): 25.38350 14.98650 14.69800 number of atom coordinates read : 2703 total number of charged atoms : 2556 net assigned charge : 5.445022 assigned positive charge : 411.5585 centred at (gu) : 90.18827 91.38621 87.27648 assigned negative charge : -406.1145 centred at (gu) : 90.19334 91.12701 87.49495 start vw surface at 0.1800000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 60139 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24594 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18187 mr = 40117 m= 1783 mr = 12077 m= 63 mr = 736 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 27241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 332 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 19681 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) : 0.5543099 object centre at (A) : 25.38350 14.98650 14.69800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3342234E-02 5.6571704E-03 midg,1,midg; midg,igrid,midg -1.1806955E-03 3.7151859E-03 1,midg,midg; igrid,midg,midg -5.7212166E-03 -4.1284468E-03 gauss-seidel spectral radius is 0.9982300 estimated iterations to convergence 189 setup time was (sec) 0.7600000 now iterating at: 14:36:50 rms-change max change #iterations 3.282014 163.2197 at 10iterations 1.385937 52.82272 at 20iterations 0.5823740 21.26575 at 30iterations 0.2455502 9.960106 at 40iterations 0.1032645 3.598661 at 50iterations 4.3366525E-02 1.556065 at 60iterations 1.8405072E-02 0.6872704 at 70iterations 7.7685607E-03 0.2938557 at 80iterations 3.2743972E-03 0.1179733 at 90iterations 1.3881186E-03 5.3321123E-02 at 100iterations 5.8927579E-04 2.1629333E-02 at 110iterations 2.4923784E-04 8.7890625E-03 at 120iterations finished qdiffx linear iterations at : 14:36:56 total time elapsed so far: 7.250000 # loops : 120 mean,max change (kT/e) : 2.4923784E-04 8.7890625E-03 energy calculations done at 7.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.440000 DelPhi exited at 14:36:57 7.446u 0.199s 0:07.93 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 Sun Oct 9 2011 at 14:36:57 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2703 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: SEP 329 has a net charge of -0.4750 !!! WARNING: GLM 356 has a net charge of -0.0940 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: 2.494395 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): 0.1330000 50.63400 ymin,ymax (A): -9.988999 39.96200 zmin,zma (A): -17.41400 46.81000 x,y,z range (A): 50.50100 49.95100 64.22400 scale (grids/A): 2.494395 object centre (A): 25.38350 14.98650 14.69800 number of atom coordinates read : 2703 total number of charged atoms : 2556 net assigned charge : 5.445022 assigned positive charge : 411.5585 centred at (gu) : 90.28223 92.07903 85.91463 assigned negative charge : -406.1145 centred at (gu) : 90.28989 91.69048 86.24241 start vw surface at 0.1600000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 139348 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24594 grid for indexing accessible points = 1.400000 m= 63312 mr = 98255 m= 17540 mr = 49067 m= 2729 mr = 12657 m= 209 mr = 1625 m= 5 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.100000 number of dielectric boundary points 61462 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 20423 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) : 1.662930 object centre at (A) : 25.38350 14.98650 14.69800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.155477 0.1172182 midg,1,midg; midg,igrid,midg -2.8661208E-02 1.0300521E-02 1,midg,midg; igrid,midg,midg -7.5990565E-02 -6.9803029E-02 gauss-seidel spectral radius is 0.9991447 estimated iterations to convergence 270 setup time was (sec) 1.420000 now iterating at: 14:36:58 rms-change max change #iterations 8.506682 339.9819 at 10iterations 4.824664 123.8273 at 20iterations 2.721849 74.49492 at 30iterations 1.525305 38.90759 at 40iterations 0.8518637 18.31220 at 50iterations 0.4754277 11.84931 at 60iterations 0.2637570 5.823961 at 70iterations 0.1466314 3.368826 at 80iterations 8.1203356E-02 1.879992 at 90iterations 4.4874314E-02 1.015213 at 100iterations 2.4793211E-02 0.5521717 at 110iterations 1.3740220E-02 0.3374434 at 120iterations 7.5863381E-03 0.1677871 at 130iterations 4.2044763E-03 8.5380554E-02 at 140iterations 2.3340550E-03 4.9439430E-02 at 150iterations 1.2951131E-03 2.7011871E-02 at 160iterations 7.2541047E-04 1.5214920E-02 at 170iterations 4.0990414E-04 8.8653564E-03 at 180iterations finished qdiffx linear iterations at : 14:37:08 total time elapsed so far: 11.58000 # loops : 180 mean,max change (kT/e) : 4.0990414E-04 8.8653564E-03 energy calculations done at 11.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.78000 DelPhi exited at 14:37:09 11.778u 0.190s 0:12.26 97.5% 0+0k 0+0io 0pf+0w