Tue Oct 11 07:57:31 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 Tue Oct 11 2011 at 07:57:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2490 !!! WARNING: GLU 245 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5949695 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): -6.369000 53.46600 ymin,ymax (A): -22.04400 22.45700 zmin,zma (A): 8.420000 54.79900 x,y,z range (A): 59.83500 44.50100 46.37900 scale (grids/A): 0.5949695 object centre (A): 23.54850 0.2065001 31.60950 number of atom coordinates read : 2490 total number of charged atoms : 2352 net assigned charge : 6.228008 assigned positive charge : 378.1111 centred at (gu) : 89.45980 90.04192 89.79543 assigned negative charge : -371.8836 centred at (gu) : 89.48936 90.00236 89.65727 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5677 nv = 96 ne = 84 npr = 50525 no. pairs analyzed = 50525 no. exposed pairs = 2916 no. arc points = 20375 no. surface atoms = 998 nbur = 1492 mkacc time = 8.0000006E-02 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 = 1.456000 m= 245 mr = 3124 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 9.0000011E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 2782 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2226 ## 295 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7255 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0278559E-09 6.0444090E-09 midg,1,midg; midg,igrid,midg 1.0718146E-09 3.4794314E-09 1,midg,midg; igrid,midg,midg 3.5576364E-09 1.2325205E-09 gauss-seidel spectral radius is 0.9853671 estimated iterations to convergence 68 setup time was (sec) 0.3900000 now iterating at: 07:57:32 rms-change max change #iterations 0.1003175 20.25265 at 10iterations 8.6385086E-03 1.329429 at 20iterations 7.4191543E-04 0.1270046 at 30iterations 6.8144313E-05 1.0894775E-02 at 40iterations 6.7008905E-06 1.0757446E-03 at 50iterations finished qdiffx linear iterations at : 07:57:35 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 6.7008905E-06 1.0757446E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 07:57:35 3.442u 0.159s 0:03.93 91.3% 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 Tue Oct 11 2011 at 07:57:35 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 = 2490 !!! WARNING: GLU 245 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.784908 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): -6.369000 53.46600 ymin,ymax (A): -22.04400 22.45700 zmin,zma (A): 8.420000 54.79900 x,y,z range (A): 59.83500 44.50100 46.37900 scale (grids/A): 1.784908 object centre (A): 23.54850 0.2065001 31.60950 number of atom coordinates read : 2490 total number of charged atoms : 2352 net assigned charge : 6.228008 assigned positive charge : 378.1111 centred at (gu) : 88.37908 90.12550 89.38605 assigned negative charge : -371.8836 centred at (gu) : 88.46812 90.00691 88.97176 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 62132 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20375 grid for indexing accessible points = 1.400000 m= 20787 mr = 43203 m= 2577 mr = 15101 m= 115 mr = 1476 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 972 time to turn everything in is 0.3100000 number of dielectric boundary points 25812 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 252 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 18292 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) : 0.5949695 object centre at (A) : 23.54850 0.2065001 31.60950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0308203E-02 2.5221679E-02 midg,1,midg; midg,igrid,midg -1.6885692E-03 4.7193812E-03 1,midg,midg; igrid,midg,midg 3.2048017E-02 2.7109902E-02 gauss-seidel spectral radius is 0.9984300 estimated iterations to convergence 200 setup time was (sec) 0.5300000 now iterating at: 07:57:36 rms-change max change #iterations 3.584009 175.1414 at 10iterations 1.592076 62.48205 at 20iterations 0.7066365 25.50005 at 30iterations 0.3128148 12.03269 at 40iterations 0.1392279 5.097676 at 50iterations 6.1600868E-02 2.454987 at 60iterations 2.7467174E-02 1.162785 at 70iterations 1.2204070E-02 0.4225349 at 80iterations 5.4185544E-03 0.1799164 at 90iterations 2.4024979E-03 8.3129883E-02 at 100iterations 1.0694697E-03 3.6596537E-02 at 110iterations 4.7566576E-04 1.7173767E-02 at 120iterations finished qdiffx linear iterations at : 07:57:43 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 4.7566576E-04 1.7173767E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 07:57:44 7.758u 0.197s 0:08.43 94.1% 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 07:57:44 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 = 2490 !!! WARNING: GLU 245 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.677363 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): -6.369000 53.46600 ymin,ymax (A): -22.04400 22.45700 zmin,zma (A): 8.420000 54.79900 x,y,z range (A): 59.83500 44.50100 46.37900 scale (grids/A): 2.677363 object centre (A): 23.54850 0.2065001 31.60950 number of atom coordinates read : 2490 total number of charged atoms : 2352 net assigned charge : 6.228008 assigned positive charge : 378.1111 centred at (gu) : 87.56844 90.18815 89.07891 assigned negative charge : -371.8836 centred at (gu) : 87.70211 90.01019 88.45767 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 143957 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20375 grid for indexing accessible points = 1.400000 m= 69938 mr = 104554 m= 22200 mr = 57269 m= 4435 mr = 17465 m= 552 mr = 3135 m= 12 mr = 352 m= 0 mr = 2 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 3363 time to turn everything in is 0.7600000 number of dielectric boundary points 58317 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 18809 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) : 1.784908 object centre at (A) : 23.54850 0.2065001 31.60950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1469684 0.3277324 midg,1,midg; midg,igrid,midg -2.1535955E-02 1.5911073E-03 1,midg,midg; igrid,midg,midg 0.3035393 0.2706344 gauss-seidel spectral radius is 0.9991916 estimated iterations to convergence 278 setup time was (sec) 0.9900000 now iterating at: 07:57:45 rms-change max change #iterations 8.623376 287.8260 at 10iterations 4.899057 121.9026 at 20iterations 2.762720 63.35487 at 30iterations 1.550715 35.23031 at 40iterations 0.8724884 19.47181 at 50iterations 0.4887058 10.80897 at 60iterations 0.2736892 5.906907 at 70iterations 0.1531069 3.113823 at 80iterations 8.6311854E-02 1.683701 at 90iterations 4.8184879E-02 1.088728 at 100iterations 2.7021131E-02 0.5659256 at 110iterations 1.5084855E-02 0.2997627 at 120iterations 8.4678018E-03 0.1724663 at 130iterations 4.7407364E-03 9.5963478E-02 at 140iterations 2.6603353E-03 5.4301739E-02 at 150iterations 1.4891371E-03 2.8141022E-02 at 160iterations 8.3407166E-04 1.7037988E-02 at 170iterations 4.6961248E-04 1.1165619E-02 at 180iterations finished qdiffx linear iterations at : 07:57:56 total time elapsed so far: 11.87000 # loops : 180 mean,max change (kT/e) : 4.6961248E-04 1.1165619E-02 energy calculations done at 11.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.00000 DelPhi exited at 07:57:56 12.004u 0.213s 0:12.54 97.3% 0+0k 0+0io 0pf+0w