Mon Oct 10 14:16:54 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 14:16:54 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3983 !!! WARNING: ADP 663 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5281899 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): -16.24000 51.16000 ymin,ymax (A): -15.92100 47.58900 zmin,zma (A): -1.505000 51.37000 x,y,z range (A): 67.40000 63.50999 52.87500 scale (grids/A): 0.5281899 object centre (A): 17.46000 15.83400 24.93250 number of atom coordinates read : 3983 total number of charged atoms : 3799 net assigned charge : -10.49999 assigned positive charge : 619.8974 centred at (gu) : 90.81971 89.72774 89.81152 assigned negative charge : -630.4006 centred at (gu) : 90.70598 89.75654 89.85970 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7347 nv = 96 ne = 84 npr = 75617 no. pairs analyzed = 75617 no. exposed pairs = 6015 no. arc points = 41444 no. surface atoms = 1991 nbur = 1992 mkacc time = 0.2600000 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 = 1.624000 m= 306 mr = 3369 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 4280 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4040 ## 573 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 9564 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0116637E-10 -5.2792326E-10 midg,1,midg; midg,igrid,midg -2.0063980E-10 -4.3045020E-10 1,midg,midg; igrid,midg,midg -7.0712525E-10 2.6025793E-10 gauss-seidel spectral radius is 0.9816214 estimated iterations to convergence 61 setup time was (sec) 0.8200000 now iterating at: 14:16:56 rms-change max change #iterations 7.3065780E-02 12.03740 at 10iterations 5.2922955E-03 0.9652748 at 20iterations 1.1486153E-03 0.1573753 at 30iterations 4.4108566E-04 5.2194595E-02 at 40iterations 1.7464851E-04 2.0374298E-02 at 50iterations finished qdiffx linear iterations at : 14:16:59 total time elapsed so far: 4.550000 # loops : 50 mean,max change (kT/e) : 1.7464851E-04 2.0374298E-02 energy calculations done at 4.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.770000 DelPhi exited at 14:17:00 4.776u 0.409s 0:05.60 92.3% 0+0k 0+0io 6pf+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 14:17:00 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3983 !!! WARNING: ADP 663 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.584570 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): -16.24000 51.16000 ymin,ymax (A): -15.92100 47.58900 zmin,zma (A): -1.505000 51.37000 x,y,z range (A): 67.40000 63.50999 52.87500 scale (grids/A): 1.584570 object centre (A): 17.46000 15.83400 24.93250 number of atom coordinates read : 3983 total number of charged atoms : 3799 net assigned charge : -10.49999 assigned positive charge : 619.8974 centred at (gu) : 92.45772 89.18219 89.43330 assigned negative charge : -630.4006 centred at (gu) : 92.11762 89.26923 89.57854 start vw surface at 0.2000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 81356 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41444 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 23708 mr = 52173 m= 2301 mr = 14391 m= 61 mr = 849 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8700000 number of dielectric boundary points 40013 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 449 ## 4 charges are in solution ## iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 28769 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) : 0.5281899 object centre at (A) : 17.46000 15.83400 24.93250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5191683E-03 -2.2408290E-02 midg,1,midg; midg,igrid,midg 9.2924322E-04 7.6620285E-03 1,midg,midg; igrid,midg,midg -3.4803119E-02 4.0793521E-03 gauss-seidel spectral radius is 0.9982017 estimated iterations to convergence 187 setup time was (sec) 1.200000 now iterating at: 14:17:02 rms-change max change #iterations 3.794219 160.0005 at 10iterations 1.586026 60.70857 at 20iterations 0.6609296 21.08313 at 30iterations 0.2757236 9.691055 at 40iterations 0.1159260 3.994892 at 50iterations 4.8408765E-02 1.606316 at 60iterations 2.0487120E-02 0.6988945 at 70iterations 8.7610772E-03 0.3130198 at 80iterations 3.9321277E-03 0.1246005 at 90iterations 1.9225137E-03 5.9003830E-02 at 100iterations 1.0712297E-03 3.6405563E-02 at 110iterations 6.7676645E-04 1.8867493E-02 at 120iterations finished qdiffx linear iterations at : 14:17:11 total time elapsed so far: 10.62000 # loops : 120 mean,max change (kT/e) : 6.7676645E-04 1.8867493E-02 energy calculations done at 10.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.83000 DelPhi exited at 14:17:12 10.831u 0.483s 0:11.88 95.2% 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 Mon Oct 10 2011 at 14:17:12 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3983 !!! WARNING: ADP 663 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.376855 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): -16.24000 51.16000 ymin,ymax (A): -15.92100 47.58900 zmin,zma (A): -1.505000 51.37000 x,y,z range (A): 67.40000 63.50999 52.87500 scale (grids/A): 2.376855 object centre (A): 17.46000 15.83400 24.93250 number of atom coordinates read : 3983 total number of charged atoms : 3799 net assigned charge : -10.49999 assigned positive charge : 619.8974 centred at (gu) : 93.68610 88.77278 89.14967 assigned negative charge : -630.4006 centred at (gu) : 93.17636 88.90367 89.36775 start vw surface at 0.1900000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 189207 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41444 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 83071 mr = 129544 m= 22066 mr = 61132 m= 3281 mr = 14976 m= 205 mr = 1770 m= 3 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 1.310000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.090000 number of dielectric boundary points 90356 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 43 iepsmp to db, and charging done at 2.260000 number of grid points assigned charge 30345 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) : 1.584570 object centre at (A) : 17.46000 15.83400 24.93250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9165126E-02 -0.3585970 midg,1,midg; midg,igrid,midg 6.6655599E-02 0.1787360 1,midg,midg; igrid,midg,midg -0.8299812 -7.1634308E-02 gauss-seidel spectral radius is 0.9991927 estimated iterations to convergence 278 setup time was (sec) 2.460000 now iterating at: 14:17:15 rms-change max change #iterations 10.38993 384.0855 at 10iterations 6.136693 160.7464 at 20iterations 3.587181 99.54315 at 30iterations 2.075676 48.76323 at 40iterations 1.194698 25.48616 at 50iterations 0.6843008 15.60805 at 60iterations 0.3909267 10.03458 at 70iterations 0.2222110 5.341125 at 80iterations 0.1260284 2.737425 at 90iterations 7.1650341E-02 1.505219 at 100iterations 4.0479593E-02 0.8212023 at 110iterations 2.2918778E-02 0.5592289 at 120iterations 1.3001214E-02 0.2646942 at 130iterations 7.3786569E-03 0.1651154 at 140iterations 4.2067454E-03 8.6387634E-02 at 150iterations 2.4264876E-03 5.4626465E-02 at 160iterations 1.4298324E-03 3.0586243E-02 at 170iterations 8.7283755E-04 1.7372131E-02 at 180iterations finished qdiffx linear iterations at : 14:17:31 total time elapsed so far: 18.03000 # loops : 180 mean,max change (kT/e) : 8.7283755E-04 1.7372131E-02 energy calculations done at 18.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.24000 DelPhi exited at 14:17:31 18.245u 0.502s 0:19.07 98.2% 0+0k 0+0io 0pf+0w