Tue Nov 22 14:12:49 PST 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 Nov 22 2011 at 14:12:51 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 0.5793139 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): -25.78000 35.67200 ymin,ymax (A): -18.81800 20.66100 zmin,zma (A): -4.224000 38.36000 x,y,z range (A): 61.45200 39.47900 42.58400 scale (grids/A): 0.5793139 object centre (A): 4.946001 0.9215002 17.06800 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.0260 centred at (gu) : 89.96231 90.19979 90.83412 assigned negative charge : -288.0262 centred at (gu) : 89.98222 90.26942 90.94659 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 4422 nv = 96 ne = 84 npr = 40183 no. pairs analyzed = 40183 no. exposed pairs = 2453 no. arc points = 17411 no. surface atoms = 830 nbur = 1134 mkacc time = 9.0000004E-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 = 1.512000 m= 169 mr = 2348 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 2229 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1814 ## 212 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 5473 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8139210E-09 -1.1451605E-09 midg,1,midg; midg,igrid,midg 1.5466383E-09 -3.3790029E-10 1,midg,midg; igrid,midg,midg 9.4301222E-10 3.7680023E-10 gauss-seidel spectral radius is 0.9845373 estimated iterations to convergence 66 setup time was (sec) 0.4300000 now iterating at: 14:12:52 rms-change max change #iterations 7.6613970E-02 13.47770 at 10iterations 6.0086376E-03 1.188656 at 20iterations 4.7429770E-04 8.2649231E-02 at 30iterations 3.5739336E-05 7.2093010E-03 at 40iterations 2.7998494E-06 5.2642822E-04 at 50iterations finished qdiffx linear iterations at : 14:12:57 total time elapsed so far: 2.860000 # loops : 50 mean,max change (kT/e) : 2.7998494E-06 5.2642822E-04 energy calculations done at 2.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.020000 DelPhi exited at 14:13:00 3.028u 0.139s 0:09.32 33.7% 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 Nov 22 2011 at 14:13:02 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 1.737942 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): -25.78000 35.67200 ymin,ymax (A): -18.81800 20.66100 zmin,zma (A): -4.224000 38.36000 x,y,z range (A): 61.45200 39.47900 42.58400 scale (grids/A): 1.737942 object centre (A): 4.946001 0.9215002 17.06800 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.0260 centred at (gu) : 89.88721 90.59922 92.50237 assigned negative charge : -288.0262 centred at (gu) : 89.94681 90.80857 92.83994 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 48086 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17411 grid for indexing accessible points = 1.400000 m= 16114 mr = 32486 m= 1812 mr = 11993 m= 52 mr = 1011 m= 0 mr = 21 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1514 time to turn everything in is 0.3300000 number of dielectric boundary points 20553 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 190 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 14195 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) : 0.5793139 object centre at (A) : 4.946001 0.9215002 17.06800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5559943E-03 -4.9692746E-03 midg,1,midg; midg,igrid,midg 2.3240531E-03 -8.4188854E-04 1,midg,midg; igrid,midg,midg 3.1535137E-02 1.9660506E-02 gauss-seidel spectral radius is 0.9982848 estimated iterations to convergence 192 setup time was (sec) 0.6400000 now iterating at: 14:13:09 rms-change max change #iterations 3.004652 167.7349 at 10iterations 1.273625 56.52164 at 20iterations 0.5476489 25.43603 at 30iterations 0.2338416 9.885715 at 40iterations 9.9712811E-02 3.828983 at 50iterations 4.2598218E-02 1.798991 at 60iterations 1.8162396E-02 0.7173462 at 70iterations 7.7466764E-03 0.3132706 at 80iterations 3.3039926E-03 0.1514959 at 90iterations 1.4120404E-03 5.9516907E-02 at 100iterations 6.0313754E-04 2.6001930E-02 at 110iterations 2.5859062E-04 9.8524094E-03 at 120iterations finished qdiffx linear iterations at : 14:13:30 total time elapsed so far: 7.260000 # loops : 120 mean,max change (kT/e) : 2.5859062E-04 9.8524094E-03 energy calculations done at 7.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.440000 DelPhi exited at 14:13:35 7.438u 0.250s 0:33.61 22.8% 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 Tue Nov 22 2011 at 14:13:37 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 2.606913 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): -25.78000 35.67200 ymin,ymax (A): -18.81800 20.66100 zmin,zma (A): -4.224000 38.36000 x,y,z range (A): 61.45200 39.47900 42.58400 scale (grids/A): 2.606913 object centre (A): 4.946001 0.9215002 17.06800 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.0260 centred at (gu) : 89.83080 90.89869 93.75343 assigned negative charge : -288.0262 centred at (gu) : 89.92035 91.21287 94.25991 start vw surface at 0.1100000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 111247 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17411 grid for indexing accessible points = 1.400000 m= 54320 mr = 78999 m= 17182 mr = 44533 m= 2776 mr = 13849 m= 196 mr = 1971 m= 11 mr = 117 m= 0 mr = 6 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 5379 time to turn everything in is 0.7900000 number of dielectric boundary points 46257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 14646 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) : 1.737942 object centre at (A) : 4.946001 0.9215002 17.06800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6586597E-02 -5.2411906E-02 midg,1,midg; midg,igrid,midg 2.1898974E-02 -6.0296622E-03 1,midg,midg; igrid,midg,midg 0.3979492 0.2005087 gauss-seidel spectral radius is 0.9991389 estimated iterations to convergence 269 setup time was (sec) 1.080000 now iterating at: 14:13:43 rms-change max change #iterations 7.334954 273.3123 at 10iterations 4.066994 124.7813 at 20iterations 2.238594 60.94002 at 30iterations 1.231933 30.82395 at 40iterations 0.6756576 15.43147 at 50iterations 0.3715242 8.720817 at 60iterations 0.2034975 4.548737 at 70iterations 0.1114539 2.752867 at 80iterations 6.1049990E-02 1.381081 at 90iterations 3.3523910E-02 0.8006136 at 100iterations 1.8330412E-02 0.4229279 at 110iterations 1.0060092E-02 0.2252760 at 120iterations 5.5098203E-03 0.1247139 at 130iterations 3.0161520E-03 6.6793442E-02 at 140iterations 1.6561045E-03 3.8612366E-02 at 150iterations 9.0585108E-04 2.1931648E-02 at 160iterations 4.9731234E-04 1.2450218E-02 at 170iterations 2.7279111E-04 6.5536499E-03 at 180iterations finished qdiffx linear iterations at : 14:14:14 total time elapsed so far: 11.55000 # loops : 180 mean,max change (kT/e) : 2.7279111E-04 6.5536499E-03 energy calculations done at 11.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.72000 DelPhi exited at 14:14:18 11.727u 0.190s 0:41.55 28.6% 0+0k 0+0io 0pf+0w