Sun Oct 9 16:03:58 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 16:03:58 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 = 3114 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: 0.6301332 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): -15.24200 37.22100 ymin,ymax (A): 55.58300 108.5770 zmin,zma (A): -5.276000 51.22000 x,y,z range (A): 52.46300 52.99400 56.49600 scale (grids/A): 0.6301332 object centre (A): 10.98950 82.08000 22.97200 number of atom coordinates read : 3114 total number of charged atoms : 2969 net assigned charge : -3.499984 assigned positive charge : 462.5240 centred at (gu) : 90.18318 88.43897 91.26877 assigned negative charge : -466.0255 centred at (gu) : 90.21122 88.34129 91.33035 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8022 nv = 96 ne = 84 npr = 64865 no. pairs analyzed = 64865 no. exposed pairs = 3785 no. arc points = 26362 no. surface atoms = 1292 nbur = 1822 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 459 mr = 4360 m= 0 mr = 60 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.3700000 number of dielectric boundary points 4061 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2586 ## 269 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 10004 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2058928E-09 -1.3322173E-08 midg,1,midg; midg,igrid,midg -1.9737724E-08 4.7343240E-09 1,midg,midg; igrid,midg,midg -5.3830579E-10 -6.7618164E-09 gauss-seidel spectral radius is 0.9869969 estimated iterations to convergence 72 setup time was (sec) 0.6100000 now iterating at: 16:03:58 rms-change max change #iterations 0.1537478 22.30006 at 10iterations 1.4701308E-02 1.888494 at 20iterations 1.4086397E-03 0.1739941 at 30iterations 1.3706634E-04 1.6252518E-02 at 40iterations 1.4449453E-05 1.9626617E-03 at 50iterations finished qdiffx linear iterations at : 16:04:01 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.4449453E-05 1.9626617E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 16:04:02 3.465u 0.134s 0:03.88 92.5% 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 16:04:02 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3114 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 1.890399 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): -15.24200 37.22100 ymin,ymax (A): 55.58300 108.5770 zmin,zma (A): -5.276000 51.22000 x,y,z range (A): 52.46300 52.99400 56.49600 scale (grids/A): 1.890399 object centre (A): 10.98950 82.08000 22.97200 number of atom coordinates read : 3114 total number of charged atoms : 2969 net assigned charge : -3.499984 assigned positive charge : 462.5240 centred at (gu) : 90.54876 85.31624 93.80560 assigned negative charge : -466.0255 centred at (gu) : 90.63345 85.02379 93.99099 start vw surface at 0.2400000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 87009 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26362 grid for indexing accessible points = 1.400000 m= 31168 mr = 60574 m= 5341 mr = 22423 m= 322 mr = 3228 m= 2 mr = 113 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7300000 number of dielectric boundary points 37504 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 166 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 23336 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) : 0.6301332 object centre at (A) : 10.98950 82.08000 22.97200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7833307E-02 9.7410958E-03 midg,1,midg; midg,igrid,midg -1.9360632E-02 -7.0862384E-03 1,midg,midg; igrid,midg,midg -3.4105804E-02 -3.3022128E-02 gauss-seidel spectral radius is 0.9986580 estimated iterations to convergence 216 setup time was (sec) 1.060000 now iterating at: 16:04:03 rms-change max change #iterations 4.650289 193.3030 at 10iterations 2.180687 78.74873 at 20iterations 1.025674 34.90411 at 30iterations 0.4820048 13.68234 at 40iterations 0.2276465 6.599476 at 50iterations 0.1072179 3.227270 at 60iterations 5.0492078E-02 1.562726 at 70iterations 2.3851076E-02 0.7137451 at 80iterations 1.1218118E-02 0.3507309 at 90iterations 5.2940785E-03 0.1523695 at 100iterations 2.5031778E-03 7.3120117E-02 at 110iterations 1.1838727E-03 3.3689499E-02 at 120iterations finished qdiffx linear iterations at : 16:04:09 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 1.1838727E-03 3.3689499E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 16:04:10 7.871u 0.194s 0:08.34 96.6% 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 Sun Oct 9 2011 at 16:04:10 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 = 3114 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.835599 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): -15.24200 37.22100 ymin,ymax (A): 55.58300 108.5770 zmin,zma (A): -5.276000 51.22000 x,y,z range (A): 52.46300 52.99400 56.49600 scale (grids/A): 2.835599 object centre (A): 10.98950 82.08000 22.97200 number of atom coordinates read : 3114 total number of charged atoms : 2969 net assigned charge : -3.499984 assigned positive charge : 462.5240 centred at (gu) : 90.82292 82.97412 95.70821 assigned negative charge : -466.0255 centred at (gu) : 90.95005 82.53548 95.98644 start vw surface at 0.2200000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 201407 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26362 grid for indexing accessible points = 1.400000 m= 99787 mr = 146893 m= 37159 mr = 80504 m= 9604 mr = 29272 m= 1420 mr = 7064 m= 89 mr = 917 m= 0 mr = 26 time to grow re-entrant surface = 1.000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.740000 number of dielectric boundary points 84790 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 23751 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) : 1.890399 object centre at (A) : 10.98950 82.08000 22.97200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4858272 0.2396969 midg,1,midg; midg,igrid,midg -0.2039934 -0.2372355 1,midg,midg; igrid,midg,midg -0.4036198 -0.3532424 gauss-seidel spectral radius is 0.9992730 estimated iterations to convergence 293 setup time was (sec) 2.090000 now iterating at: 16:04:12 rms-change max change #iterations 10.97120 374.6949 at 10iterations 6.469923 132.1807 at 20iterations 3.799725 68.75381 at 30iterations 2.224666 40.56164 at 40iterations 1.295364 23.65910 at 50iterations 0.7546347 14.30464 at 60iterations 0.4383960 7.461365 at 70iterations 0.2543680 4.916372 at 80iterations 0.1478878 2.484581 at 90iterations 8.5618183E-02 1.522934 at 100iterations 4.9550485E-02 0.9358649 at 110iterations 2.8683433E-02 0.5677624 at 120iterations 1.6635980E-02 0.2785101 at 130iterations 9.6222693E-03 0.1656456 at 140iterations 5.5855089E-03 9.1447830E-02 at 150iterations 3.2507153E-03 6.1641693E-02 at 160iterations 1.8899561E-03 3.1730652E-02 at 170iterations 1.1144200E-03 2.1184921E-02 at 180iterations finished qdiffx linear iterations at : 16:04:23 total time elapsed so far: 12.67000 # loops : 180 mean,max change (kT/e) : 1.1144200E-03 2.1184921E-02 energy calculations done at 12.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 16:04:23 12.905u 0.210s 0:13.42 97.6% 0+0k 0+0io 0pf+0w