Tue Oct 11 03:24:26 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 Tue Oct 11 2011 at 03:24:26 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3852 !!! WARNING: HIR 61 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5213826 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): -37.55100 29.69800 ymin,ymax (A): -42.04200 20.24900 zmin,zma (A): -44.76800 23.51200 x,y,z range (A): 67.24900 62.29100 68.28000 scale (grids/A): 0.5213826 object centre (A): -3.926501 -10.89650 -10.62800 number of atom coordinates read : 3852 total number of charged atoms : 3710 net assigned charge : -5.485967 assigned positive charge : 575.4814 centred at (gu) : 89.92419 89.54771 87.76205 assigned negative charge : -580.9697 centred at (gu) : 89.87027 89.56190 87.71028 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7039 nv = 96 ne = 84 npr = 74419 no. pairs analyzed = 74419 no. exposed pairs = 5272 no. arc points = 37638 no. surface atoms = 1763 nbur = 2089 mkacc time = 0.1700000 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 = 1.652000 m= 265 mr = 3442 m= 0 mr = 5 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3857 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3734 ## 554 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 9221 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.2265231E-10 2.5977401E-11 midg,1,midg; midg,igrid,midg -8.1606652E-11 -1.4845898E-10 1,midg,midg; igrid,midg,midg -3.0432420E-10 5.5306801E-11 gauss-seidel spectral radius is 0.9811363 estimated iterations to convergence 60 setup time was (sec) 0.6700000 now iterating at: 03:24:27 rms-change max change #iterations 6.9492713E-02 10.25201 at 10iterations 4.3535847E-03 0.7246542 at 20iterations 5.0107471E-04 7.5902939E-02 at 30iterations 1.2899688E-04 2.2676468E-02 at 40iterations 3.7250826E-05 6.8759918E-03 at 50iterations finished qdiffx linear iterations at : 03:24:30 total time elapsed so far: 4.120000 # loops : 50 mean,max change (kT/e) : 3.7250826E-05 6.8759918E-03 energy calculations done at 4.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.300000 DelPhi exited at 03:24:31 4.306u 0.228s 0:04.88 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 Tue Oct 11 2011 at 03:24:31 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3852 !!! WARNING: HIR 61 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.564148 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): -37.55100 29.69800 ymin,ymax (A): -42.04200 20.24900 zmin,zma (A): -44.76800 23.51200 x,y,z range (A): 67.24900 62.29100 68.28000 scale (grids/A): 1.564148 object centre (A): -3.926501 -10.89650 -10.62800 number of atom coordinates read : 3852 total number of charged atoms : 3710 net assigned charge : -5.485967 assigned positive charge : 575.4814 centred at (gu) : 89.77158 88.64214 83.28542 assigned negative charge : -580.9697 centred at (gu) : 89.61034 88.68523 83.13040 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 77813 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37638 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 23495 mr = 50854 m= 2264 mr = 15753 m= 61 mr = 950 m= 0 mr = 3 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1175 time to turn everything in is 0.5900000 number of dielectric boundary points 36073 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 465 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 28070 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) : 0.5213826 object centre at (A) : -3.926501 -10.89650 -10.62800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2978787E-02 9.2934025E-03 midg,1,midg; midg,igrid,midg -4.6403413E-03 -3.5150030E-03 1,midg,midg; igrid,midg,midg -4.1536766E-04 2.1361912E-02 gauss-seidel spectral radius is 0.9981337 estimated iterations to convergence 184 setup time was (sec) 0.9700000 now iterating at: 03:24:32 rms-change max change #iterations 3.534816 163.4779 at 10iterations 1.443955 56.42084 at 20iterations 0.5938528 20.22605 at 30iterations 0.2447646 8.242907 at 40iterations 0.1005717 4.135696 at 50iterations 4.1525651E-02 1.475264 at 60iterations 1.7124051E-02 0.5410252 at 70iterations 7.1220300E-03 0.2466602 at 80iterations 3.0027716E-03 0.1144066 at 90iterations 1.3046521E-03 4.3868542E-02 at 100iterations 6.0443504E-04 2.3025990E-02 at 110iterations 3.0665702E-04 1.1291504E-02 at 120iterations finished qdiffx linear iterations at : 03:24:41 total time elapsed so far: 9.940000 # loops : 120 mean,max change (kT/e) : 3.0665702E-04 1.1291504E-02 energy calculations done at 9.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.13000 DelPhi exited at 03:24:42 10.134u 0.291s 0:10.78 96.6% 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 Tue Oct 11 2011 at 03:24:42 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3852 !!! WARNING: HIR 61 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.346221 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): -37.55100 29.69800 ymin,ymax (A): -42.04200 20.24900 zmin,zma (A): -44.76800 23.51200 x,y,z range (A): 67.24900 62.29100 68.28000 scale (grids/A): 2.346221 object centre (A): -3.926501 -10.89650 -10.62800 number of atom coordinates read : 3852 total number of charged atoms : 3710 net assigned charge : -5.485967 assigned positive charge : 575.4814 centred at (gu) : 89.65723 87.96294 79.92778 assigned negative charge : -580.9697 centred at (gu) : 89.41545 88.02776 79.69539 start vw surface at 0.1800000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 180543 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37638 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 82009 mr = 125054 m= 22382 mr = 63727 m= 3236 mr = 16297 m= 209 mr = 1858 m= 3 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 4111 time to turn everything in is 1.440000 number of dielectric boundary points 81383 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 50 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 29606 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) : 1.564148 object centre at (A) : -3.926501 -10.89650 -10.62800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2696833 0.1696063 midg,1,midg; midg,igrid,midg -3.5814825E-02 -1.0221228E-02 1,midg,midg; igrid,midg,midg 7.3567480E-02 0.7637902 gauss-seidel spectral radius is 0.9991590 estimated iterations to convergence 272 setup time was (sec) 1.800000 now iterating at: 03:24:44 rms-change max change #iterations 9.501276 300.3995 at 10iterations 5.409491 135.0521 at 20iterations 3.066734 83.78014 at 30iterations 1.727296 37.32159 at 40iterations 0.9695336 22.65079 at 50iterations 0.5409352 11.12803 at 60iterations 0.3036230 6.323246 at 70iterations 0.1692128 3.965569 at 80iterations 9.4041429E-02 1.871639 at 90iterations 5.2345164E-02 1.074924 at 100iterations 2.9088952E-02 0.5543461 at 110iterations 1.6167413E-02 0.3006859 at 120iterations 8.9892186E-03 0.1859398 at 130iterations 4.9827765E-03 0.1057606 at 140iterations 2.7815236E-03 5.7346344E-02 at 150iterations 1.5533660E-03 3.2054901E-02 at 160iterations 8.7364047E-04 1.8325329E-02 at 170iterations 4.9888348E-04 1.0364532E-02 at 180iterations finished qdiffx linear iterations at : 03:24:58 total time elapsed so far: 15.65000 # loops : 180 mean,max change (kT/e) : 4.9888348E-04 1.0364532E-02 energy calculations done at 15.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.83000 DelPhi exited at 03:24:58 15.830u 0.279s 0:16.42 98.0% 0+0k 0+0io 0pf+0w