Sat Oct 15 13:15:46 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 Sat Oct 15 2011 at 13:15:46 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5384 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 0.5021157 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): 3.357000 68.38700 ymin,ymax (A): -8.946000 53.69500 zmin,zma (A): -2.281000 68.61900 x,y,z range (A): 65.03000 62.64100 70.89999 scale (grids/A): 0.5021157 object centre (A): 35.87200 22.37450 33.16900 number of atom coordinates read : 5384 total number of charged atoms : 5226 net assigned charge : 5.740033 assigned positive charge : 825.6530 centred at (gu) : 88.15514 89.33547 88.71737 assigned negative charge : -819.9191 centred at (gu) : 88.07745 89.36414 88.65472 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 8703 nv = 96 ne = 84 npr = 108916 no. pairs analyzed = 108916 no. exposed pairs = 6278 no. arc points = 43241 no. surface atoms = 2148 nbur = 3236 mkacc time = 0.2500000 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 = 1.708000 m= 306 mr = 4793 m= 0 mr = 8 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 4208 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4237 ## 583 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 11613 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.9674768E-11 1.3274186E-10 midg,1,midg; midg,igrid,midg 1.4114152E-10 1.2065734E-12 1,midg,midg; igrid,midg,midg -1.6915580E-10 1.3286026E-10 gauss-seidel spectral radius is 0.9797564 estimated iterations to convergence 58 setup time was (sec) 0.7700000 now iterating at: 13:15:47 rms-change max change #iterations 7.1484089E-02 9.665432 at 10iterations 9.5509151E-03 1.573029 at 20iterations 3.8609514E-03 0.6974640 at 30iterations 1.7229154E-03 0.3093033 at 40iterations 7.7539805E-04 0.1369705 at 50iterations finished qdiffx linear iterations at : 13:15:51 total time elapsed so far: 4.310000 # loops : 50 mean,max change (kT/e) : 7.7539805E-04 0.1369705 energy calculations done at 4.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.480000 DelPhi exited at 13:15:51 4.479u 0.272s 0:05.19 91.3% 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 Sat Oct 15 2011 at 13:15:51 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5384 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 1.506347 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): 3.357000 68.38700 ymin,ymax (A): -8.946000 53.69500 zmin,zma (A): -2.281000 68.61900 x,y,z range (A): 65.03000 62.64100 70.89999 scale (grids/A): 1.506347 object centre (A): 35.87200 22.37450 33.16900 number of atom coordinates read : 5384 total number of charged atoms : 5226 net assigned charge : 5.740033 assigned positive charge : 825.6530 centred at (gu) : 84.46394 88.00513 86.15091 assigned negative charge : -819.9191 centred at (gu) : 84.23226 88.09230 85.96407 start vw surface at 0.2200000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 99022 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43241 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 30709 mr = 70953 m= 2824 mr = 21243 m= 41 mr = 1243 m= 0 mr = 4 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7300000 number of dielectric boundary points 39153 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 572 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 39074 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) : 0.5021157 object centre at (A) : 35.87200 22.37450 33.16900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0788289E-02 1.5572128E-02 midg,1,midg; midg,igrid,midg 1.1945599E-02 4.1379775E-03 1,midg,midg; igrid,midg,midg -8.9900391E-03 4.8761964E-03 gauss-seidel spectral radius is 0.9980828 estimated iterations to convergence 182 setup time was (sec) 1.070000 now iterating at: 13:15:53 rms-change max change #iterations 3.962394 144.2907 at 10iterations 1.610694 51.36400 at 20iterations 0.6576688 19.99379 at 30iterations 0.2682418 8.118250 at 40iterations 0.1106614 3.258187 at 50iterations 4.6448160E-02 1.643215 at 60iterations 2.0644527E-02 0.6982803 at 70iterations 1.0281584E-02 0.3705215 at 80iterations 6.0757040E-03 0.2133217 at 90iterations 4.0455214E-03 0.1387291 at 100iterations 2.8903121E-03 9.6282959E-02 at 110iterations 2.1102605E-03 7.0251465E-02 at 120iterations finished qdiffx linear iterations at : 13:16:02 total time elapsed so far: 9.990000 # loops : 120 mean,max change (kT/e) : 2.1102605E-03 7.0251465E-02 energy calculations done at 9.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.18000 DelPhi exited at 13:16:02 10.178u 0.286s 0:10.93 95.6% 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 Sat Oct 15 2011 at 13:16:02 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5384 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 2.259521 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): 3.357000 68.38700 ymin,ymax (A): -8.946000 53.69500 zmin,zma (A): -2.281000 68.61900 x,y,z range (A): 65.03000 62.64100 70.89999 scale (grids/A): 2.259521 object centre (A): 35.87200 22.37450 33.16900 number of atom coordinates read : 5384 total number of charged atoms : 5226 net assigned charge : 5.740033 assigned positive charge : 825.6530 centred at (gu) : 81.69550 87.00688 84.22606 assigned negative charge : -819.9191 centred at (gu) : 81.34833 87.13841 83.94599 start vw surface at 0.2000000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 230936 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43241 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 109365 mr = 173563 m= 29137 mr = 87743 m= 4034 mr = 21584 m= 209 mr = 2491 m= 0 mr = 72 time to grow re-entrant surface = 1.100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.800000 number of dielectric boundary points 88228 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 79 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 41653 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) : 1.506347 object centre at (A) : 35.87200 22.37450 33.16900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2963047 0.5476944 midg,1,midg; midg,igrid,midg 0.2189838 3.3798516E-02 1,midg,midg; igrid,midg,midg -0.2431058 7.4868552E-02 gauss-seidel spectral radius is 0.9991555 estimated iterations to convergence 272 setup time was (sec) 2.160000 now iterating at: 13:16:05 rms-change max change #iterations 10.72366 326.5137 at 10iterations 6.098505 135.3674 at 20iterations 3.438207 66.67071 at 30iterations 1.935584 48.58108 at 40iterations 1.083870 20.51849 at 50iterations 0.6045619 11.59601 at 60iterations 0.3377139 6.026180 at 70iterations 0.1878632 3.564514 at 80iterations 0.1049191 1.860409 at 90iterations 5.8633201E-02 1.032812 at 100iterations 3.3065896E-02 0.6783905 at 110iterations 1.8850220E-02 0.3578110 at 120iterations 1.1060747E-02 0.2590027 at 130iterations 6.8136365E-03 0.1445160 at 140iterations 4.4744164E-03 9.3055725E-02 at 150iterations 3.1742614E-03 6.9763184E-02 at 160iterations 2.3852934E-03 4.9392700E-02 at 170iterations 1.8659837E-03 3.7742615E-02 at 180iterations finished qdiffx linear iterations at : 13:16:20 total time elapsed so far: 16.76000 # loops : 180 mean,max change (kT/e) : 1.8659837E-03 3.7742615E-02 energy calculations done at 16.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.94000 DelPhi exited at 13:16:20 16.942u 0.321s 0:17.61 98.0% 0+0k 0+0io 0pf+0w