Sun Oct 9 15:19:04 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 15:19:05 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 = 5492 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5286998 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): -18.85600 48.47900 ymin,ymax (A): -108.4660 -43.14500 zmin,zma (A): -29.95400 32.85400 x,y,z range (A): 67.33500 65.32100 62.80800 scale (grids/A): 0.5286998 object centre (A): 14.81150 -75.80550 1.450000 number of atom coordinates read : 5492 total number of charged atoms : 5320 net assigned charge : -4.499955 assigned positive charge : 839.1802 centred at (gu) : 89.62724 90.15444 91.52896 assigned negative charge : -843.6873 centred at (gu) : 89.72010 90.18632 91.56134 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 9537 nv = 96 ne = 84 npr = 112215 no. pairs analyzed = 112215 no. exposed pairs = 6467 no. arc points = 44947 no. surface atoms = 2176 nbur = 3316 mkacc time = 0.1900000 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 = 1.596000 m= 320 mr = 5215 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 64 time to turn everything in is 0.3600000 number of dielectric boundary points 4630 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4382 ## 625 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 12865 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6027151E-11 -5.1450982E-10 midg,1,midg; midg,igrid,midg 6.4533552E-11 -3.5783221E-10 1,midg,midg; igrid,midg,midg 5.0164251E-10 -6.7617345E-10 gauss-seidel spectral radius is 0.9817434 estimated iterations to convergence 61 setup time was (sec) 0.5400000 now iterating at: 15:19:05 rms-change max change #iterations 8.6845428E-02 12.83247 at 10iterations 6.8199686E-03 0.8966827 at 20iterations 1.5014890E-03 0.2806129 at 30iterations 5.0699891E-04 9.6374512E-02 at 40iterations 1.7503728E-04 3.3504486E-02 at 50iterations finished qdiffx linear iterations at : 15:19:08 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 1.7503728E-04 3.3504486E-02 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 15:19:09 3.591u 0.181s 0:04.05 93.0% 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 Sun Oct 9 2011 at 15:19:09 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 = 5492 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: 1.586099 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): -18.85600 48.47900 ymin,ymax (A): -108.4660 -43.14500 zmin,zma (A): -29.95400 32.85400 x,y,z range (A): 67.33500 65.32100 62.80800 scale (grids/A): 1.586099 object centre (A): 14.81150 -75.80550 1.450000 number of atom coordinates read : 5492 total number of charged atoms : 5320 net assigned charge : -4.499955 assigned positive charge : 839.1802 centred at (gu) : 88.87998 90.46151 94.58549 assigned negative charge : -843.6873 centred at (gu) : 89.16015 90.55858 94.68377 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 109022 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44947 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 32951 mr = 77519 m= 3207 mr = 22950 m= 74 mr = 1495 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 3270 time to turn everything in is 0.5100000 number of dielectric boundary points 43287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 516 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 40365 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) : 0.5286998 object centre at (A) : 14.81150 -75.80550 1.450000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.7801646E-03 -2.3897460E-03 midg,1,midg; midg,igrid,midg -9.2160981E-03 -3.0636812E-02 1,midg,midg; igrid,midg,midg 7.0385723E-03 -5.8893254E-03 gauss-seidel spectral radius is 0.9983065 estimated iterations to convergence 193 setup time was (sec) 0.7400000 now iterating at: 15:19:10 rms-change max change #iterations 4.510635 170.4884 at 10iterations 1.941689 58.79737 at 20iterations 0.8340226 25.54748 at 30iterations 0.3586293 10.89011 at 40iterations 0.1549145 4.413002 at 50iterations 6.7163765E-02 1.824768 at 60iterations 2.9169459E-02 0.8488774 at 70iterations 1.2857976E-02 0.3902168 at 80iterations 5.7897931E-03 0.1745758 at 90iterations 2.7443548E-03 9.0034485E-02 at 100iterations 1.4004902E-03 4.7241211E-02 at 110iterations 7.8138919E-04 2.7713776E-02 at 120iterations finished qdiffx linear iterations at : 15:19:17 total time elapsed so far: 8.010000 # loops : 120 mean,max change (kT/e) : 7.8138919E-04 2.7713776E-02 energy calculations done at 8.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.150000 DelPhi exited at 15:19:17 8.150u 0.216s 0:08.69 96.2% 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 Sun Oct 9 2011 at 15:19:17 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 = 5492 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: 2.379149 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): -18.85600 48.47900 ymin,ymax (A): -108.4660 -43.14500 zmin,zma (A): -29.95400 32.85400 x,y,z range (A): 67.33500 65.32100 62.80800 scale (grids/A): 2.379149 object centre (A): 14.81150 -75.80550 1.450000 number of atom coordinates read : 5492 total number of charged atoms : 5320 net assigned charge : -4.499955 assigned positive charge : 839.1802 centred at (gu) : 88.31985 90.69180 96.87817 assigned negative charge : -843.6873 centred at (gu) : 88.74027 90.83774 97.02556 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 254568 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44947 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 116251 mr = 189668 m= 31279 mr = 93012 m= 4868 mr = 23473 m= 309 mr = 3179 m= 6 mr = 107 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 10867 time to turn everything in is 1.280000 number of dielectric boundary points 97842 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 48 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 42503 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) : 1.586099 object centre at (A) : 14.81150 -75.80550 1.450000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2227844 3.8333856E-02 midg,1,midg; midg,igrid,midg -0.1153196 -0.5700695 1,midg,midg; igrid,midg,midg 0.1312101 9.2032149E-02 gauss-seidel spectral radius is 0.9992242 estimated iterations to convergence 283 setup time was (sec) 1.520000 now iterating at: 15:19:19 rms-change max change #iterations 11.78701 311.1759 at 10iterations 6.856076 153.0031 at 20iterations 3.948451 69.28094 at 30iterations 2.269127 41.06561 at 40iterations 1.300650 23.22430 at 50iterations 0.7426717 13.56657 at 60iterations 0.4241395 6.865250 at 70iterations 0.2416435 4.499930 at 80iterations 0.1377491 2.359742 at 90iterations 7.8196272E-02 1.274225 at 100iterations 4.4550169E-02 0.7201614 at 110iterations 2.5292648E-02 0.3969574 at 120iterations 1.4398725E-02 0.2424622 at 130iterations 8.2176989E-03 0.1337376 at 140iterations 4.6913521E-03 7.8437805E-02 at 150iterations 2.6891474E-03 4.7044754E-02 at 160iterations 1.5561661E-03 2.9155731E-02 at 170iterations 9.1439689E-04 1.5394211E-02 at 180iterations finished qdiffx linear iterations at : 15:19:31 total time elapsed so far: 13.46000 # loops : 180 mean,max change (kT/e) : 9.1439689E-04 1.5394211E-02 energy calculations done at 13.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.58000 DelPhi exited at 15:19:31 13.586u 0.225s 0:14.08 98.0% 0+0k 0+0io 0pf+0w