Sun Oct 9 08:48:28 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 Sun Oct 9 2011 at 08:48:28 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 = 5859 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5005625 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): 3.773000 74.89300 ymin,ymax (A): 17.68400 85.56100 zmin,zma (A): 6.552000 75.18800 x,y,z range (A): 71.12000 67.87700 68.63600 scale (grids/A): 0.5005625 object centre (A): 39.33300 51.62250 40.87000 number of atom coordinates read : 5859 total number of charged atoms : 5689 net assigned charge : -4.999976 assigned positive charge : 879.2352 centred at (gu) : 89.88833 89.15079 89.21853 assigned negative charge : -884.2427 centred at (gu) : 89.81387 89.12292 89.15933 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 9149 nv = 96 ne = 84 npr = 118383 no. pairs analyzed = 118383 no. exposed pairs = 7341 no. arc points = 50509 no. surface atoms = 2452 nbur = 3407 mkacc time = 0.2000000 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= 299 mr = 4691 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 4754 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4890 ## 738 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 12397 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0589931E-10 6.3247574E-11 midg,1,midg; midg,igrid,midg -1.2688539E-10 1.1151225E-11 1,midg,midg; igrid,midg,midg -2.0489817E-10 1.0627429E-10 gauss-seidel spectral radius is 0.9796687 estimated iterations to convergence 58 setup time was (sec) 0.5800000 now iterating at: 08:48:29 rms-change max change #iterations 6.7803442E-02 8.644219 at 10iterations 3.7754280E-03 0.5482063 at 20iterations 3.6129807E-04 8.0511093E-02 at 30iterations 8.9767003E-05 2.1276474E-02 at 40iterations 2.7219392E-05 6.1149597E-03 at 50iterations finished qdiffx linear iterations at : 08:48:32 total time elapsed so far: 3.680000 # loops : 50 mean,max change (kT/e) : 2.7219392E-05 6.1149597E-03 energy calculations done at 3.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.800000 DelPhi exited at 08:48:32 3.801u 0.229s 0:04.39 91.5% 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 Sun Oct 9 2011 at 08:48:33 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 = 5859 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.501687 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): 3.773000 74.89300 ymin,ymax (A): 17.68400 85.56100 zmin,zma (A): 6.552000 75.18800 x,y,z range (A): 71.12000 67.87700 68.63600 scale (grids/A): 1.501687 object centre (A): 39.33300 51.62250 40.87000 number of atom coordinates read : 5859 total number of charged atoms : 5689 net assigned charge : -4.999976 assigned positive charge : 879.2352 centred at (gu) : 89.66282 87.45076 87.65385 assigned negative charge : -884.2427 centred at (gu) : 89.44168 87.36840 87.47736 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 104397 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50509 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 29005 mr = 71570 m= 2265 mr = 18788 m= 25 mr = 919 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 1279 time to turn everything in is 0.5100000 number of dielectric boundary points 44415 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 752 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 42383 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) : 0.5005625 object centre at (A) : 39.33300 51.62250 40.87000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4232188E-02 -1.0082367E-02 midg,1,midg; midg,igrid,midg -6.4131389E-03 -2.0459222E-03 1,midg,midg; igrid,midg,midg -9.7315190E-03 2.1914868E-02 gauss-seidel spectral radius is 0.9981268 estimated iterations to convergence 184 setup time was (sec) 0.7400000 now iterating at: 08:48:33 rms-change max change #iterations 4.087784 196.9950 at 10iterations 1.688106 51.08503 at 20iterations 0.6935586 22.24428 at 30iterations 0.2859545 8.347540 at 40iterations 0.1180240 3.636223 at 50iterations 4.8653543E-02 1.480543 at 60iterations 2.0101145E-02 0.6071444 at 70iterations 8.3199991E-03 0.2588867 at 80iterations 3.4394707E-03 0.1050892 at 90iterations 1.4326110E-03 4.5780182E-02 at 100iterations 6.0084992E-04 1.8173218E-02 at 110iterations 2.5898564E-04 8.9569092E-03 at 120iterations finished qdiffx linear iterations at : 08:48:41 total time elapsed so far: 8.310000 # loops : 120 mean,max change (kT/e) : 2.5898564E-04 8.9569092E-03 energy calculations done at 8.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.440000 DelPhi exited at 08:48:42 8.442u 0.226s 0:09.03 95.9% 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 Sun Oct 9 2011 at 08:48:42 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 = 5859 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.252531 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): 3.773000 74.89300 ymin,ymax (A): 17.68400 85.56100 zmin,zma (A): 6.552000 75.18800 x,y,z range (A): 71.12000 67.87700 68.63600 scale (grids/A): 2.252531 object centre (A): 39.33300 51.62250 40.87000 number of atom coordinates read : 5859 total number of charged atoms : 5689 net assigned charge : -4.999976 assigned positive charge : 879.2352 centred at (gu) : 89.49390 86.17590 86.48038 assigned negative charge : -884.2427 centred at (gu) : 89.16247 86.05242 86.21593 start vw surface at 0.1400000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 243768 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50509 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 106457 mr = 176557 m= 24670 mr = 81902 m= 2990 mr = 17370 m= 125 mr = 1843 m= 0 mr = 38 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 4333 time to turn everything in is 1.250000 number of dielectric boundary points 100300 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 122 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 45344 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) : 1.501687 object centre at (A) : 39.33300 51.62250 40.87000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3893319 -0.1849380 midg,1,midg; midg,igrid,midg -0.1669707 -2.1971337E-02 1,midg,midg; igrid,midg,midg -2.1497067E-02 0.5584034 gauss-seidel spectral radius is 0.9991973 estimated iterations to convergence 279 setup time was (sec) 1.520000 now iterating at: 08:48:43 rms-change max change #iterations 11.29665 271.9506 at 10iterations 6.571861 156.2487 at 20iterations 3.801974 85.69003 at 30iterations 2.186488 45.30121 at 40iterations 1.253239 25.83424 at 50iterations 0.7181481 13.72006 at 60iterations 0.4095010 7.128204 at 70iterations 0.2325543 4.424265 at 80iterations 0.1324837 2.413823 at 90iterations 7.5120345E-02 1.354307 at 100iterations 4.2488884E-02 0.7488651 at 110iterations 2.4106642E-02 0.4174356 at 120iterations 1.3623031E-02 0.2490582 at 130iterations 7.7119917E-03 0.1331367 at 140iterations 4.3536425E-03 8.6025953E-02 at 150iterations 2.4595889E-03 4.2854309E-02 at 160iterations 1.3870437E-03 2.3002625E-02 at 170iterations 7.8459620E-04 1.4245749E-02 at 180iterations finished qdiffx linear iterations at : 08:48:56 total time elapsed so far: 14.35000 # loops : 180 mean,max change (kT/e) : 7.8459620E-04 1.4245749E-02 energy calculations done at 14.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.48000 DelPhi exited at 08:48:57 14.482u 0.240s 0:15.01 98.0% 0+0k 0+0io 0pf+0w