Tue Oct 11 03:17:22 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+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 Oct 11 2011 at 03:17:22 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3282 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5549666 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): 19.59900 83.74700 ymin,ymax (A): 80.83000 134.9360 zmin,zma (A): 3.791000 52.96900 x,y,z range (A): 64.14800 54.10599 49.17800 scale (grids/A): 0.5549666 object centre (A): 51.67300 107.8830 28.38000 number of atom coordinates read : 3282 total number of charged atoms : 3135 net assigned charge : -10.49999 assigned positive charge : 490.7173 centred at (gu) : 90.16333 89.79948 89.72334 assigned negative charge : -501.2185 centred at (gu) : 90.20564 89.59514 89.86265 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6702 nv = 96 ne = 84 npr = 64793 no. pairs analyzed = 64793 no. exposed pairs = 4383 no. arc points = 30832 no. surface atoms = 1448 nbur = 1834 mkacc time = 0.1100000 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= 316 mr = 3438 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.2300000 number of dielectric boundary points 3568 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3102 ## 375 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8698 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.4820698E-10 -2.2432214E-09 midg,1,midg; midg,igrid,midg -3.2644099E-09 1.1010840E-09 1,midg,midg; igrid,midg,midg -4.6359094E-10 -1.4186551E-09 gauss-seidel spectral radius is 0.9832852 estimated iterations to convergence 64 setup time was (sec) 0.4200000 now iterating at: 03:17:23 rms-change max change #iterations 8.7881856E-02 16.12750 at 10iterations 6.1858823E-03 1.069204 at 20iterations 5.4920447E-04 0.1144943 at 30iterations 1.0951680E-04 3.2350540E-02 at 40iterations 3.1277235E-05 9.6302032E-03 at 50iterations finished qdiffx linear iterations at : 03:17:26 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 3.1277235E-05 9.6302032E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 03:17:26 3.388u 0.161s 0:03.90 90.7% 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 03:17:26 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3282 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.664900 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): 19.59900 83.74700 ymin,ymax (A): 80.83000 134.9360 zmin,zma (A): 3.791000 52.96900 x,y,z range (A): 64.14800 54.10599 49.17800 scale (grids/A): 1.664900 object centre (A): 51.67300 107.8830 28.38000 number of atom coordinates read : 3282 total number of charged atoms : 3135 net assigned charge : -10.49999 assigned positive charge : 490.7173 centred at (gu) : 90.48917 89.39748 89.16868 assigned negative charge : -501.2185 centred at (gu) : 90.61635 88.78500 89.58762 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 74208 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30832 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 23523 mr = 49948 m= 2675 mr = 16285 m= 76 mr = 1350 m= 0 mr = 5 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 2333 time to turn everything in is 0.3600000 number of dielectric boundary points 32894 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 338 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 24104 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) : 0.5549666 object centre at (A) : 51.67300 107.8830 28.38000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4529534E-05 -1.1965283E-02 midg,1,midg; midg,igrid,midg -3.3790525E-02 4.4460925E-03 1,midg,midg; igrid,midg,midg -1.3178012E-02 -1.4109042E-02 gauss-seidel spectral radius is 0.9982992 estimated iterations to convergence 193 setup time was (sec) 0.5600000 now iterating at: 03:17:27 rms-change max change #iterations 3.697809 167.3746 at 10iterations 1.574262 57.48601 at 20iterations 0.6716587 22.54062 at 30iterations 0.2862912 9.623642 at 40iterations 0.1225943 4.164256 at 50iterations 5.2724157E-02 1.757271 at 60iterations 2.2674972E-02 0.7576842 at 70iterations 9.7099403E-03 0.3382826 at 80iterations 4.1653980E-03 0.1549258 at 90iterations 1.8056232E-03 6.8325043E-02 at 100iterations 7.8561326E-04 2.5466919E-02 at 110iterations 3.4827736E-04 1.3172150E-02 at 120iterations finished qdiffx linear iterations at : 03:17:34 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 3.4827736E-04 1.3172150E-02 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 03:17:34 7.652u 0.199s 0:08.16 96.0% 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 03:17:34 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3282 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.497350 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): 19.59900 83.74700 ymin,ymax (A): 80.83000 134.9360 zmin,zma (A): 3.791000 52.96900 x,y,z range (A): 64.14800 54.10599 49.17800 scale (grids/A): 2.497350 object centre (A): 51.67300 107.8830 28.38000 number of atom coordinates read : 3282 total number of charged atoms : 3135 net assigned charge : -10.49999 assigned positive charge : 490.7173 centred at (gu) : 90.73331 89.09582 88.75291 assigned negative charge : -501.2185 centred at (gu) : 90.92429 88.17734 89.38136 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 172333 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30832 grid for indexing accessible points = 1.400000 m= 80051 mr = 122285 m= 24046 mr = 62937 m= 4207 mr = 18346 m= 301 mr = 2796 m= 3 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 7670 time to turn everything in is 0.8600000 number of dielectric boundary points 74461 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 25049 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) : 1.664900 object centre at (A) : 51.67300 107.8830 28.38000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3217482E-03 -0.1557155 midg,1,midg; midg,igrid,midg -0.4589309 5.8159772E-02 1,midg,midg; igrid,midg,midg -0.1688262 -4.4294126E-02 gauss-seidel spectral radius is 0.9991854 estimated iterations to convergence 277 setup time was (sec) 1.090000 now iterating at: 03:17:36 rms-change max change #iterations 9.439179 274.8943 at 10iterations 5.370472 142.9997 at 20iterations 3.034614 63.60086 at 30iterations 1.709638 35.75555 at 40iterations 0.9610719 18.52182 at 50iterations 0.5394530 12.61635 at 60iterations 0.3016621 5.879640 at 70iterations 0.1690416 3.459354 at 80iterations 9.4442949E-02 1.888582 at 90iterations 5.2880052E-02 1.057198 at 100iterations 2.9613007E-02 0.5934911 at 110iterations 1.6553355E-02 0.3410883 at 120iterations 9.2410101E-03 0.1844254 at 130iterations 5.1623001E-03 0.1063080 at 140iterations 2.8857582E-03 5.3887367E-02 at 150iterations 1.6167010E-03 3.0727386E-02 at 160iterations 9.0250163E-04 2.0095825E-02 at 170iterations 5.0661125E-04 1.0154724E-02 at 180iterations finished qdiffx linear iterations at : 03:17:47 total time elapsed so far: 12.19000 # loops : 180 mean,max change (kT/e) : 5.0661125E-04 1.0154724E-02 energy calculations done at 12.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.33000 DelPhi exited at 03:17:47 12.329u 0.196s 0:12.82 97.5% 0+0k 0+0io 0pf+0w