Sat Oct 15 13:37:32 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+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 Sat Oct 15 2011 at 13:37:32 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2128 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7383288 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): -20.63200 24.59200 ymin,ymax (A): -7.970000 37.63200 zmin,zma (A): -3.502000 44.71500 x,y,z range (A): 45.22400 45.60200 48.21700 scale (grids/A): 0.7383288 object centre (A): 1.980000 14.83100 20.60650 number of atom coordinates read : 2128 total number of charged atoms : 1989 net assigned charge : -4.999980 assigned positive charge : 319.1439 centred at (gu) : 88.67046 90.04688 89.96033 assigned negative charge : -324.1440 centred at (gu) : 88.73100 90.08739 90.16679 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7951 nv = 96 ne = 84 npr = 43876 no. pairs analyzed = 43876 no. exposed pairs = 2732 no. arc points = 19366 no. surface atoms = 926 nbur = 1202 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 569 mr = 4377 m= 6 mr = 115 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.1800000 number of dielectric boundary points 4034 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1603 ## 148 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8445 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1636761E-07 -2.9253562E-07 midg,1,midg; midg,igrid,midg -4.5132985E-08 -1.2706029E-07 1,midg,midg; igrid,midg,midg -3.1653990E-08 -1.1434884E-07 gauss-seidel spectral radius is 0.9904437 estimated iterations to convergence 83 setup time was (sec) 0.3800000 now iterating at: 13:37:33 rms-change max change #iterations 0.2467031 33.94648 at 10iterations 3.2781016E-02 4.606812 at 20iterations 4.3456657E-03 0.5212971 at 30iterations 5.9103483E-04 7.3465347E-02 at 40iterations 7.9486090E-05 9.6316338E-03 at 50iterations finished qdiffx linear iterations at : 13:37:36 total time elapsed so far: 3.520000 # loops : 50 mean,max change (kT/e) : 7.9486090E-05 9.6316338E-03 energy calculations done at 3.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.660000 DelPhi exited at 13:37:36 3.666u 0.180s 0:04.34 88.4% 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 15 2011 at 13:37:36 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2128 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.214987 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): -20.63200 24.59200 ymin,ymax (A): -7.970000 37.63200 zmin,zma (A): -3.502000 44.71500 x,y,z range (A): 45.22400 45.60200 48.21700 scale (grids/A): 2.214987 object centre (A): 1.980000 14.83100 20.60650 number of atom coordinates read : 2128 total number of charged atoms : 1989 net assigned charge : -4.999980 assigned positive charge : 319.1439 centred at (gu) : 86.01146 90.14071 89.88101 assigned negative charge : -324.1440 centred at (gu) : 86.19308 90.26221 90.50036 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 83634 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19366 grid for indexing accessible points = 1.400000 m= 32961 mr = 57147 m= 7169 mr = 24995 m= 769 mr = 5008 m= 24 mr = 438 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 270 time to turn everything in is 0.4400000 number of dielectric boundary points 36969 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 42 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 15845 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) : 0.7383288 object centre at (A) : 1.980000 14.83100 20.60650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6695893E-03 -0.1331849 midg,1,midg; midg,igrid,midg -2.9574921E-02 -2.5884217E-02 1,midg,midg; igrid,midg,midg -1.4388812E-02 7.1133296E-03 gauss-seidel spectral radius is 0.9989240 estimated iterations to convergence 241 setup time was (sec) 0.6700000 now iterating at: 13:37:38 rms-change max change #iterations 5.087881 235.5652 at 10iterations 2.575853 93.73891 at 20iterations 1.309328 39.32506 at 30iterations 0.6663010 19.73006 at 40iterations 0.3386232 9.552758 at 50iterations 0.1724317 4.868079 at 60iterations 8.8027574E-02 2.603766 at 70iterations 4.4825643E-02 1.218059 at 80iterations 2.2828385E-02 0.6744099 at 90iterations 1.1595572E-02 0.3118505 at 100iterations 5.9181629E-03 0.1688528 at 110iterations 3.0251411E-03 8.3658218E-02 at 120iterations finished qdiffx linear iterations at : 13:37:46 total time elapsed so far: 8.430000 # loops : 120 mean,max change (kT/e) : 3.0251411E-03 8.3658218E-02 energy calculations done at 8.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.570000 DelPhi exited at 13:37:47 8.571u 0.241s 0:10.38 84.8% 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 15 2011 at 13:37:47 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2128 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.322480 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): -20.63200 24.59200 ymin,ymax (A): -7.970000 37.63200 zmin,zma (A): -3.502000 44.71500 x,y,z range (A): 45.22400 45.60200 48.21700 scale (grids/A): 3.322480 object centre (A): 1.980000 14.83100 20.60650 number of atom coordinates read : 2128 total number of charged atoms : 1989 net assigned charge : -4.999980 assigned positive charge : 319.1439 centred at (gu) : 84.01717 90.21092 89.82149 assigned negative charge : -324.1440 centred at (gu) : 84.28959 90.39341 90.75049 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 192257 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19366 grid for indexing accessible points = 1.400000 m= 101400 mr = 137693 m= 43121 mr = 83725 m= 13826 mr = 35600 m= 3339 mr = 11108 m= 507 mr = 2568 m= 23 mr = 370 m= 0 mr = 2 time to grow re-entrant surface = 0.6800001 no. cavity mid-points inaccessible to solvent = 697 time to turn everything in is 1.350000 number of dielectric boundary points 83407 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 15912 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) : 2.214987 object centre at (A) : 1.980000 14.83100 20.60650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1042835 -1.182963 midg,1,midg; midg,igrid,midg -0.2612099 -0.1182520 1,midg,midg; igrid,midg,midg -0.2790573 -1.0217864E-02 gauss-seidel spectral radius is 0.9993178 estimated iterations to convergence 302 setup time was (sec) 1.620000 now iterating at: 13:37:49 rms-change max change #iterations 10.95450 282.3351 at 10iterations 6.469287 145.1188 at 20iterations 3.811923 69.09901 at 30iterations 2.242112 41.80776 at 40iterations 1.322132 21.97334 at 50iterations 0.7787731 13.16883 at 60iterations 0.4577235 7.410599 at 70iterations 0.2689543 4.589674 at 80iterations 0.1580620 2.551112 at 90iterations 9.2838243E-02 1.496239 at 100iterations 5.4523706E-02 0.9394188 at 110iterations 3.1936843E-02 0.5219479 at 120iterations 1.8788490E-02 0.2944397 at 130iterations 1.1035861E-02 0.1881113 at 140iterations 6.4616241E-03 0.1096039 at 150iterations 3.7952650E-03 5.8231354E-02 at 160iterations 2.2286302E-03 3.5154343E-02 at 170iterations 1.3091459E-03 2.1634102E-02 at 180iterations finished qdiffx linear iterations at : 13:38:04 total time elapsed so far: 14.40000 # loops : 180 mean,max change (kT/e) : 1.3091459E-03 2.1634102E-02 energy calculations done at 14.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.53000 DelPhi exited at 13:38:05 14.535u 0.267s 0:17.92 82.5% 0+0k 0+0io 0pf+0w