Tue Oct 11 07:16:41 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 07:16:41 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: 243 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3326 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5637729 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): 0.4590000 48.62200 ymin,ymax (A): -8.611000 49.27900 zmin,zma (A): -2.403000 60.74300 x,y,z range (A): 48.16300 57.89000 63.14600 scale (grids/A): 0.5637729 object centre (A): 24.54050 20.33400 29.17000 number of atom coordinates read : 3326 total number of charged atoms : 3176 net assigned charge : -0.9999899 assigned positive charge : 500.3296 centred at (gu) : 89.76762 89.75089 91.40596 assigned negative charge : -501.3308 centred at (gu) : 89.69735 89.70045 91.41508 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6779 nv = 96 ne = 84 npr = 69405 no. pairs analyzed = 69405 no. exposed pairs = 3960 no. arc points = 26887 no. surface atoms = 1354 nbur = 1972 mkacc time = 0.1700000 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 = 1.540000 m= 288 mr = 3782 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.3900000 number of dielectric boundary points 3274 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2856 ## 335 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8909 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.1095959E-12 -3.4372397E-10 midg,1,midg; midg,igrid,midg -8.9049884E-10 5.6369531E-10 1,midg,midg; igrid,midg,midg -1.1904540E-09 8.2906942E-10 gauss-seidel spectral radius is 0.9837890 estimated iterations to convergence 65 setup time was (sec) 0.6200000 now iterating at: 07:16:42 rms-change max change #iterations 8.9068666E-02 14.97018 at 10iterations 6.7677912E-03 1.079781 at 20iterations 7.1102724E-04 0.1213970 at 30iterations 1.2498135E-04 2.5123596E-02 at 40iterations 2.8015429E-05 5.7392120E-03 at 50iterations finished qdiffx linear iterations at : 07:16:44 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 2.8015429E-05 5.7392120E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 07:16:45 3.411u 0.154s 0:04.01 88.7% 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 Oct 11 2011 at 07:16:45 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: 243 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3326 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.691319 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): 0.4590000 48.62200 ymin,ymax (A): -8.611000 49.27900 zmin,zma (A): -2.403000 60.74300 x,y,z range (A): 48.16300 57.89000 63.14600 scale (grids/A): 1.691319 object centre (A): 24.54050 20.33400 29.17000 number of atom coordinates read : 3326 total number of charged atoms : 3176 net assigned charge : -0.9999899 assigned positive charge : 500.3296 centred at (gu) : 89.30177 89.25195 94.21677 assigned negative charge : -501.3308 centred at (gu) : 89.09150 89.10102 94.24483 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 75321 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26887 grid for indexing accessible points = 1.400000 m= 24962 mr = 53319 m= 2858 mr = 18086 m= 96 mr = 1552 m= 2 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1070 time to turn everything in is 0.5600000 number of dielectric boundary points 30267 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 285 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 24491 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) : 0.5637729 object centre at (A) : 24.54050 20.33400 29.17000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7207874E-02 8.4709720E-04 midg,1,midg; midg,igrid,midg -1.2316544E-02 1.5172668E-03 1,midg,midg; igrid,midg,midg -8.3346842E-03 -3.9847029E-04 gauss-seidel spectral radius is 0.9983431 estimated iterations to convergence 195 setup time was (sec) 0.8500000 now iterating at: 07:16:46 rms-change max change #iterations 3.839004 178.3270 at 10iterations 1.660825 58.45918 at 20iterations 0.7208717 24.40600 at 30iterations 0.3135700 11.66435 at 40iterations 0.1364870 4.585773 at 50iterations 5.9169825E-02 1.980530 at 60iterations 2.5818801E-02 0.9050784 at 70iterations 1.1239652E-02 0.3825631 at 80iterations 4.9219900E-03 0.1517906 at 90iterations 2.1636535E-03 7.4235916E-02 at 100iterations 9.5265673E-04 3.4444809E-02 at 110iterations 4.2970918E-04 1.4138222E-02 at 120iterations finished qdiffx linear iterations at : 07:16:52 total time elapsed so far: 7.270000 # loops : 120 mean,max change (kT/e) : 4.2970918E-04 1.4138222E-02 energy calculations done at 7.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 07:16:53 7.464u 0.177s 0:08.11 94.0% 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 07:16:53 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: 243 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3326 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.536978 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): 0.4590000 48.62200 ymin,ymax (A): -8.611000 49.27900 zmin,zma (A): -2.403000 60.74300 x,y,z range (A): 48.16300 57.89000 63.14600 scale (grids/A): 2.536978 object centre (A): 24.54050 20.33400 29.17000 number of atom coordinates read : 3326 total number of charged atoms : 3176 net assigned charge : -0.9999899 assigned positive charge : 500.3296 centred at (gu) : 88.95231 88.87771 96.32496 assigned negative charge : -501.3308 centred at (gu) : 88.63721 88.65130 96.36723 start vw surface at 0.1800000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 174930 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26887 grid for indexing accessible points = 1.400000 m= 85334 mr = 129460 m= 25704 mr = 69744 m= 4608 mr = 20037 m= 398 mr = 3249 m= 12 mr = 193 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 3551 time to turn everything in is 1.340000 number of dielectric boundary points 68303 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 25384 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) : 1.691319 object centre at (A) : 24.54050 20.33400 29.17000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5312050 -0.1545864 midg,1,midg; midg,igrid,midg -0.2128963 4.5477964E-02 1,midg,midg; igrid,midg,midg -0.1164564 3.5339955E-03 gauss-seidel spectral radius is 0.9991885 estimated iterations to convergence 277 setup time was (sec) 1.640000 now iterating at: 07:16:55 rms-change max change #iterations 9.633915 295.9126 at 10iterations 5.493199 131.6602 at 20iterations 3.104500 68.03124 at 30iterations 1.755564 38.63717 at 40iterations 0.9897305 20.27761 at 50iterations 0.5561814 10.28087 at 60iterations 0.3135263 6.290112 at 70iterations 0.1755544 3.466188 at 80iterations 9.8560564E-02 1.854302 at 90iterations 5.5077266E-02 1.000465 at 100iterations 3.0892996E-02 0.6065521 at 110iterations 1.7315017E-02 0.3483562 at 120iterations 9.7101089E-03 0.1733208 at 130iterations 5.4399143E-03 0.1024122 at 140iterations 3.0638857E-03 5.9685946E-02 at 150iterations 1.7283089E-03 3.3416748E-02 at 160iterations 9.7890163E-04 2.0471454E-02 at 170iterations 5.6003232E-04 1.1188507E-02 at 180iterations finished qdiffx linear iterations at : 07:17:05 total time elapsed so far: 11.66000 # loops : 180 mean,max change (kT/e) : 5.6003232E-04 1.1188507E-02 energy calculations done at 11.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.85000 DelPhi exited at 07:17:05 11.850u 0.174s 0:12.32 97.5% 0+0k 0+0io 0pf+0w