Mon Oct 10 13:59:14 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 Mon Oct 10 2011 at 13:59:14 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 = 4156 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5548022 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): -1.636000 60.72700 ymin,ymax (A): -15.31200 38.84000 zmin,zma (A): -19.29100 44.87600 x,y,z range (A): 62.36300 54.15200 64.16701 scale (grids/A): 0.5548022 object centre (A): 29.54550 11.76400 12.79250 number of atom coordinates read : 4156 total number of charged atoms : 4003 net assigned charge : -5.499958 assigned positive charge : 622.1719 centred at (gu) : 88.74152 90.43112 90.33887 assigned negative charge : -627.6743 centred at (gu) : 88.85067 90.51921 90.47791 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 8109 nv = 96 ne = 84 npr = 88303 no. pairs analyzed = 88303 no. exposed pairs = 4735 no. arc points = 31527 no. surface atoms = 1622 nbur = 2534 mkacc time = 0.1500000 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 = 1.512000 m= 356 mr = 4686 m= 0 mr = 26 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3753 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3246 ## 379 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 10749 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1810952E-09 -2.5211742E-09 midg,1,midg; midg,igrid,midg 5.7683042E-10 -1.8228909E-09 1,midg,midg; igrid,midg,midg 1.2570587E-09 -1.4128955E-09 gauss-seidel spectral radius is 0.9833239 estimated iterations to convergence 64 setup time was (sec) 0.4700000 now iterating at: 13:59:15 rms-change max change #iterations 9.5563337E-02 12.97943 at 10iterations 7.2338176E-03 1.076441 at 20iterations 9.6119242E-04 0.1191368 at 30iterations 2.7995947E-04 3.6045074E-02 at 40iterations 9.3844334E-05 1.2525558E-02 at 50iterations finished qdiffx linear iterations at : 13:59:18 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 9.3844334E-05 1.2525558E-02 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 13:59:19 3.556u 0.205s 0:04.38 85.6% 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 Mon Oct 10 2011 at 13:59:19 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 = 4156 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.664407 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): -1.636000 60.72700 ymin,ymax (A): -15.31200 38.84000 zmin,zma (A): -19.29100 44.87600 x,y,z range (A): 62.36300 54.15200 64.16701 scale (grids/A): 1.664407 object centre (A): 29.54550 11.76400 12.79250 number of atom coordinates read : 4156 total number of charged atoms : 4003 net assigned charge : -5.499958 assigned positive charge : 622.1719 centred at (gu) : 86.22308 91.29232 91.01526 assigned negative charge : -627.6743 centred at (gu) : 86.55151 91.55737 91.43331 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 91391 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31527 grid for indexing accessible points = 1.400000 m= 29970 mr = 66374 m= 3351 mr = 21645 m= 79 mr = 1805 m= 2 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1087 time to turn everything in is 0.4300000 number of dielectric boundary points 34962 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 324 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 30838 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) : 0.5548022 object centre at (A) : 29.54550 11.76400 12.79250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5248340E-03 -2.3295889E-02 midg,1,midg; midg,igrid,midg -1.0971558E-02 -2.5916509E-02 1,midg,midg; igrid,midg,midg 2.2502888E-02 3.4826109E-03 gauss-seidel spectral radius is 0.9983632 estimated iterations to convergence 196 setup time was (sec) 0.6600000 now iterating at: 13:59:20 rms-change max change #iterations 4.186933 159.9235 at 10iterations 1.827760 65.75987 at 20iterations 0.7973021 25.11555 at 30iterations 0.3470862 10.57559 at 40iterations 0.1528170 4.585526 at 50iterations 6.6411875E-02 2.070228 at 60iterations 2.9199651E-02 0.9205780 at 70iterations 1.2820433E-02 0.3975410 at 80iterations 5.6714495E-03 0.1775055 at 90iterations 2.5436091E-03 8.0261230E-02 at 100iterations 1.1849463E-03 3.6183357E-02 at 110iterations 5.7981157E-04 1.8141747E-02 at 120iterations finished qdiffx linear iterations at : 13:59:27 total time elapsed so far: 8.000000 # loops : 120 mean,max change (kT/e) : 5.7981157E-04 1.8141747E-02 energy calculations done at 8.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.130000 DelPhi exited at 13:59:28 8.131u 0.274s 0:08.79 95.5% 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 Mon Oct 10 2011 at 13:59:28 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 = 4156 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.496610 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): -1.636000 60.72700 ymin,ymax (A): -15.31200 38.84000 zmin,zma (A): -19.29100 44.87600 x,y,z range (A): 62.36300 54.15200 64.16701 scale (grids/A): 2.496610 object centre (A): 29.54550 11.76400 12.79250 number of atom coordinates read : 4156 total number of charged atoms : 4003 net assigned charge : -5.499958 assigned positive charge : 622.1719 centred at (gu) : 84.33423 91.93842 91.52271 assigned negative charge : -627.6743 centred at (gu) : 84.82722 92.33595 92.14983 start vw surface at 0.1100000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 212969 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31527 grid for indexing accessible points = 1.400000 m= 103504 mr = 161803 m= 30929 mr = 84638 m= 5597 mr = 24021 m= 420 mr = 3905 m= 2 mr = 199 m= 0 mr = 0 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 3599 time to turn everything in is 1.100000 number of dielectric boundary points 78855 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 31996 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) : 1.664407 object centre at (A) : 29.54550 11.76400 12.79250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2321004 -0.2834692 midg,1,midg; midg,igrid,midg -0.2284227 -0.3497005 1,midg,midg; igrid,midg,midg 0.4374118 9.8727204E-02 gauss-seidel spectral radius is 0.9992139 estimated iterations to convergence 282 setup time was (sec) 1.340000 now iterating at: 13:59:29 rms-change max change #iterations 10.70118 365.1516 at 10iterations 6.209444 122.7310 at 20iterations 3.572794 63.68388 at 30iterations 2.052809 41.83181 at 40iterations 1.171888 21.56007 at 50iterations 0.6675934 12.91801 at 60iterations 0.3795828 7.503492 at 70iterations 0.2156885 4.623444 at 80iterations 0.1225145 2.297806 at 90iterations 6.9464847E-02 1.248491 at 100iterations 3.9332617E-02 0.6957569 at 110iterations 2.2330714E-02 0.3882980 at 120iterations 1.2640326E-02 0.2221680 at 130iterations 7.1961349E-03 0.1397829 at 140iterations 4.1035204E-03 7.1483612E-02 at 150iterations 2.3580019E-03 3.9552450E-02 at 160iterations 1.3683869E-03 2.3689985E-02 at 170iterations 8.1415137E-04 1.4782906E-02 at 180iterations finished qdiffx linear iterations at : 13:59:42 total time elapsed so far: 14.09000 # loops : 180 mean,max change (kT/e) : 8.1415137E-04 1.4782906E-02 energy calculations done at 14.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.23000 DelPhi exited at 13:59:43 14.227u 0.266s 0:14.87 97.3% 0+0k 0+0io 0pf+0w