Sat Oct 8 18:23:32 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 Sat Oct 8 2011 at 18:23:33 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3287 !!! WARNING: ILE 378 has a net charge of -0.2720 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: 0.5492302 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): -13.59800 42.06100 ymin,ymax (A): -72.67000 -7.852000 zmin,zma (A): -21.87700 24.95900 x,y,z range (A): 55.65900 64.81800 46.83600 scale (grids/A): 0.5492302 object centre (A): 14.23150 -40.26100 1.540999 number of atom coordinates read : 3287 total number of charged atoms : 3142 net assigned charge : -4.771982 assigned positive charge : 488.9908 centred at (gu) : 90.45240 90.41142 90.06652 assigned negative charge : -493.7639 centred at (gu) : 90.49886 90.40346 90.05128 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6572 nv = 96 ne = 84 npr = 65774 no. pairs analyzed = 65774 no. exposed pairs = 4116 no. arc points = 28310 no. surface atoms = 1394 nbur = 1893 mkacc time = 0.1900000 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 = 1.568000 m= 264 mr = 3518 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 3308 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2913 ## 366 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 8537 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.5559262E-10 -2.1215080E-10 midg,1,midg; midg,igrid,midg -3.6432452E-10 -2.9692110E-10 1,midg,midg; igrid,midg,midg 4.2370062E-11 -8.1042784E-10 gauss-seidel spectral radius is 0.9829301 estimated iterations to convergence 63 setup time was (sec) 0.6900000 now iterating at: 18:23:34 rms-change max change #iterations 8.0538601E-02 12.67767 at 10iterations 5.5478443E-03 0.8596802 at 20iterations 3.9406770E-04 5.9700012E-02 at 30iterations 3.8653539E-05 6.4258575E-03 at 40iterations 7.1137979E-06 1.4757514E-03 at 50iterations finished qdiffx linear iterations at : 18:23:37 total time elapsed so far: 4.140000 # loops : 50 mean,max change (kT/e) : 7.1137979E-06 1.4757514E-03 energy calculations done at 4.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.330000 DelPhi exited at 18:23:37 4.331u 0.284s 0:04.88 94.4% 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 18:23:37 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3287 !!! WARNING: ILE 378 has a net charge of -0.2720 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: 1.647690 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): -13.59800 42.06100 ymin,ymax (A): -72.67000 -7.852000 zmin,zma (A): -21.87700 24.95900 x,y,z range (A): 55.65900 64.81800 46.83600 scale (grids/A): 1.647690 object centre (A): 14.23150 -40.26100 1.540999 number of atom coordinates read : 3287 total number of charged atoms : 3142 net assigned charge : -4.771982 assigned positive charge : 488.9908 centred at (gu) : 91.35606 91.23375 90.19910 assigned negative charge : -493.7639 centred at (gu) : 91.49645 91.20967 90.15342 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 72612 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28310 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 24007 mr = 50549 m= 2566 mr = 16977 m= 79 mr = 1297 m= 0 mr = 19 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 212 time to turn everything in is 0.6600000 number of dielectric boundary points 30422 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 320 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 24118 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) : 0.5492302 object centre at (A) : 14.23150 -40.26100 1.540999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8204963E-03 -3.9297319E-03 midg,1,midg; midg,igrid,midg 6.5789120E-03 1.8722387E-02 1,midg,midg; igrid,midg,midg -1.1833613E-02 -7.8412015E-03 gauss-seidel spectral radius is 0.9982517 estimated iterations to convergence 190 setup time was (sec) 0.9600000 now iterating at: 18:23:39 rms-change max change #iterations 3.589076 159.8610 at 10iterations 1.508864 53.55641 at 20iterations 0.6420219 22.72143 at 30iterations 0.2724085 8.871582 at 40iterations 0.1155056 4.314233 at 50iterations 4.8954811E-02 1.680789 at 60iterations 2.0711670E-02 0.7170486 at 70iterations 8.8133607E-03 0.2961388 at 80iterations 3.7446248E-03 0.1276960 at 90iterations 1.5958794E-03 5.7647705E-02 at 100iterations 6.8011973E-04 2.3493171E-02 at 110iterations 2.9223258E-04 1.0986328E-02 at 120iterations finished qdiffx linear iterations at : 18:23:47 total time elapsed so far: 9.650000 # loops : 120 mean,max change (kT/e) : 2.9223258E-04 1.0986328E-02 energy calculations done at 9.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.830000 DelPhi exited at 18:23:48 9.832u 0.342s 0:10.45 97.3% 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 18:23:48 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3287 !!! WARNING: ILE 378 has a net charge of -0.2720 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: 2.471536 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): -13.59800 42.06100 ymin,ymax (A): -72.67000 -7.852000 zmin,zma (A): -21.87700 24.95900 x,y,z range (A): 55.65900 64.81800 46.83600 scale (grids/A): 2.471536 object centre (A): 14.23150 -40.26100 1.540999 number of atom coordinates read : 3287 total number of charged atoms : 3142 net assigned charge : -4.771982 assigned positive charge : 488.9908 centred at (gu) : 92.03400 91.85024 90.29842 assigned negative charge : -493.7639 centred at (gu) : 92.24446 91.81440 90.22994 start vw surface at 0.1900000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 168648 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28310 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 81818 mr = 123358 m= 24522 mr = 65717 m= 4137 mr = 18769 m= 358 mr = 2711 m= 6 mr = 190 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 798 time to turn everything in is 1.640000 number of dielectric boundary points 68744 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 25111 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) : 1.647690 object centre at (A) : 14.23150 -40.26100 1.540999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.7613853E-02 -3.3411387E-02 midg,1,midg; midg,igrid,midg 0.2261053 0.5345754 1,midg,midg; igrid,midg,midg -0.2013511 -8.2319528E-02 gauss-seidel spectral radius is 0.9991642 estimated iterations to convergence 273 setup time was (sec) 1.970000 now iterating at: 18:23:50 rms-change max change #iterations 9.179317 307.4979 at 10iterations 5.192917 119.6349 at 20iterations 2.924588 64.57334 at 30iterations 1.642226 34.29989 at 40iterations 0.9196974 17.38931 at 50iterations 0.5120433 10.94089 at 60iterations 0.2857843 5.753662 at 70iterations 0.1590295 3.190003 at 80iterations 8.8527173E-02 1.655884 at 90iterations 4.9231242E-02 0.9255142 at 100iterations 2.7312022E-02 0.5205488 at 110iterations 1.5218724E-02 0.2972728 at 120iterations 8.4238211E-03 0.1785975 at 130iterations 4.7066589E-03 0.1109314 at 140iterations 2.6119738E-03 4.5977592E-02 at 150iterations 1.4514450E-03 2.8466225E-02 at 160iterations 8.1171840E-04 1.5922546E-02 at 170iterations 4.5503472E-04 9.3622208E-03 at 180iterations finished qdiffx linear iterations at : 18:24:05 total time elapsed so far: 16.38000 # loops : 180 mean,max change (kT/e) : 4.5503472E-04 9.3622208E-03 energy calculations done at 16.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.56000 DelPhi exited at 18:24:05 16.564u 0.352s 0:17.21 98.2% 0+0k 0+0io 0pf+0w