Tue Nov 22 14:11:13 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+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 Nov 22 2011 at 14:11:18 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 = 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 : 287.8260 centred at (gu) : 89.96062 90.21745 90.85960 assigned negative charge : -284.8263 centred at (gu) : 89.98367 90.29251 90.97687 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 0.3200000 number of grid points assigned charge 5473 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8426350E-09 -1.2125403E-09 midg,1,midg; midg,igrid,midg 1.6011609E-09 -4.0676210E-10 1,midg,midg; igrid,midg,midg 9.8525033E-10 3.3783454E-10 gauss-seidel spectral radius is 0.9845373 estimated iterations to convergence 66 setup time was (sec) 0.4400000 now iterating at: 14:11:21 rms-change max change #iterations 7.4023895E-02 12.71698 at 10iterations 5.8350852E-03 1.072106 at 20iterations 4.5943135E-04 7.6184273E-02 at 30iterations 3.4498989E-05 6.8769455E-03 at 40iterations 2.7066333E-06 5.0735474E-04 at 50iterations finished qdiffx linear iterations at : 14:11:29 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 2.7066333E-06 5.0735474E-04 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 14:11:31 3.110u 0.173s 0:13.67 23.9% 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 14:11:34 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 = 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 : 287.8260 centred at (gu) : 89.88213 90.65229 92.57884 assigned negative charge : -284.8263 centred at (gu) : 89.95120 90.87785 92.93080 start vw surface at 0.1100000 fill in re-entrant regions at 0.1700000 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 0.3400000 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 0.4700000 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 5.5029667E-03 -5.2907015E-03 midg,1,midg; midg,igrid,midg 2.5094282E-03 -1.0337495E-03 1,midg,midg; igrid,midg,midg 3.1533357E-02 1.9494422E-02 gauss-seidel spectral radius is 0.9982848 estimated iterations to convergence 192 setup time was (sec) 0.6200000 now iterating at: 14:11:38 rms-change max change #iterations 2.953247 167.7349 at 10iterations 1.252333 56.53126 at 20iterations 0.5381398 25.11066 at 30iterations 0.2300430 9.416710 at 40iterations 9.8079100E-02 3.633831 at 50iterations 4.1874304E-02 1.821853 at 60iterations 1.7846575E-02 0.7050171 at 70iterations 7.6129222E-03 0.3083211 at 80iterations 3.2468340E-03 0.1528554 at 90iterations 1.3878569E-03 5.6480408E-02 at 100iterations 5.9373444E-04 2.5764465E-02 at 110iterations 2.5428858E-04 9.7880363E-03 at 120iterations finished qdiffx linear iterations at : 14:11:57 total time elapsed so far: 6.690000 # loops : 120 mean,max change (kT/e) : 2.5428858E-04 9.7880363E-03 energy calculations done at 6.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.870000 DelPhi exited at 14:12:01 6.874u 0.164s 0:27.83 25.2% 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 14:12:04 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 = 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 : 287.8260 centred at (gu) : 89.82319 90.97832 93.86817 assigned negative charge : -284.8263 centred at (gu) : 89.92693 91.31680 94.39623 start vw surface at 0.1000000 fill in re-entrant regions at 0.2800000 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 = 0.4600000 no. cavity mid-points inaccessible to solvent = 5379 time to turn everything in is 0.8000000 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 0.9400000 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 5.4698359E-02 -5.6998000E-02 midg,1,midg; midg,igrid,midg 2.2430943E-02 -8.2502849E-03 1,midg,midg; igrid,midg,midg 0.3976504 0.1982771 gauss-seidel spectral radius is 0.9991389 estimated iterations to convergence 269 setup time was (sec) 1.110000 now iterating at: 14:12:10 rms-change max change #iterations 7.225536 273.3122 at 10iterations 4.005923 124.7851 at 20iterations 2.205879 62.37461 at 30iterations 1.214044 30.87691 at 40iterations 0.6660650 15.47398 at 50iterations 0.3665261 8.586539 at 60iterations 0.2005941 4.453012 at 70iterations 0.1098898 2.657886 at 80iterations 6.0214352E-02 1.340111 at 90iterations 3.3059668E-02 0.8068731 at 100iterations 1.8066891E-02 0.4108353 at 110iterations 9.9195559E-03 0.2319565 at 120iterations 5.4323212E-03 0.1253052 at 130iterations 2.9733598E-03 6.8717957E-02 at 140iterations 1.6325932E-03 3.8821220E-02 at 150iterations 8.9335395E-04 2.1221161E-02 at 160iterations 4.9018674E-04 1.2115479E-02 at 170iterations 2.6888915E-04 6.5879822E-03 at 180iterations finished qdiffx linear iterations at : 14:12:38 total time elapsed so far: 10.43000 # loops : 180 mean,max change (kT/e) : 2.6888915E-04 6.5879822E-03 energy calculations done at 10.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.61000 DelPhi exited at 14:12:42 10.615u 0.169s 0:39.16 27.5% 0+0k 0+0io 0pf+0w