Sat Oct 8 17:28:51 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 Sat Oct 8 2011 at 17:28:51 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3576 !!! WARNING: ASL 227 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5377806 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): -2.127000 64.07100 ymin,ymax (A): 14.23300 76.43300 zmin,zma (A): -13.24800 34.34000 x,y,z range (A): 66.19800 62.20000 47.58800 scale (grids/A): 0.5377806 object centre (A): 30.97200 45.33300 10.54600 number of atom coordinates read : 3576 total number of charged atoms : 3429 net assigned charge : -7.099989 assigned positive charge : 547.4420 centred at (gu) : 89.43068 87.40311 89.62715 assigned negative charge : -554.5439 centred at (gu) : 89.40950 87.42769 89.65411 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6620 nv = 96 ne = 84 npr = 72701 no. pairs analyzed = 72701 no. exposed pairs = 4336 no. arc points = 30253 no. surface atoms = 1456 nbur = 2120 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 = 1.568000 m= 246 mr = 3552 m= 0 mr = 13 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3301 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2996 ## 401 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8724 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7322149E-10 -4.4077972E-10 midg,1,midg; midg,igrid,midg -3.2040731E-10 -2.4906377E-10 1,midg,midg; igrid,midg,midg -5.1622451E-10 -1.6917298E-10 gauss-seidel spectral radius is 0.9822185 estimated iterations to convergence 62 setup time was (sec) 0.6700000 now iterating at: 17:28:52 rms-change max change #iterations 7.6915227E-02 12.39708 at 10iterations 5.0468133E-03 0.9546785 at 20iterations 3.5038489E-04 6.3173294E-02 at 30iterations 4.0642677E-05 7.2479248E-03 at 40iterations 8.3793229E-06 1.6717911E-03 at 50iterations finished qdiffx linear iterations at : 17:28:56 total time elapsed so far: 4.420000 # loops : 50 mean,max change (kT/e) : 8.3793229E-06 1.6717911E-03 energy calculations done at 4.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.590000 DelPhi exited at 17:28:56 4.594u 0.404s 0:05.26 94.8% 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 8 2011 at 17:28:56 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3576 !!! WARNING: ASL 227 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.613342 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): -2.127000 64.07100 ymin,ymax (A): 14.23300 76.43300 zmin,zma (A): -13.24800 34.34000 x,y,z range (A): 66.19800 62.20000 47.58800 scale (grids/A): 1.613342 object centre (A): 30.97200 45.33300 10.54600 number of atom coordinates read : 3576 total number of charged atoms : 3429 net assigned charge : -7.099989 assigned positive charge : 547.4420 centred at (gu) : 88.29136 82.20869 88.88073 assigned negative charge : -554.5439 centred at (gu) : 88.22789 82.28263 88.96208 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 74456 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30253 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 22695 mr = 52075 m= 2309 mr = 15727 m= 54 mr = 1147 m= 0 mr = 3 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1865 time to turn everything in is 0.6000000 number of dielectric boundary points 30562 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 334 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 26180 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) : 0.5377806 object centre at (A) : 30.97200 45.33300 10.54600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0217521E-03 -1.7576168E-03 midg,1,midg; midg,igrid,midg -2.0334024E-02 -1.5337394E-02 1,midg,midg; igrid,midg,midg 1.1369734E-02 -5.4179267E-03 gauss-seidel spectral radius is 0.9981863 estimated iterations to convergence 187 setup time was (sec) 0.8900000 now iterating at: 17:28:57 rms-change max change #iterations 3.669984 176.2358 at 10iterations 1.531268 56.05214 at 20iterations 0.6374566 22.70413 at 30iterations 0.2667831 8.897371 at 40iterations 0.1114837 3.704399 at 50iterations 4.6566863E-02 1.586784 at 60iterations 1.9432832E-02 0.6399574 at 70iterations 8.1408946E-03 0.2824402 at 80iterations 3.4108600E-03 0.1110425 at 90iterations 1.4274128E-03 5.0935745E-02 at 100iterations 5.9784506E-04 2.0656586E-02 at 110iterations 2.5239284E-04 8.0294609E-03 at 120iterations finished qdiffx linear iterations at : 17:29:07 total time elapsed so far: 10.23000 # loops : 120 mean,max change (kT/e) : 2.5239284E-04 8.0294609E-03 energy calculations done at 10.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.39000 DelPhi exited at 17:29:07 10.393u 0.452s 0:11.15 97.2% 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 Sat Oct 8 2011 at 17:29:07 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3576 !!! WARNING: ASL 227 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.420013 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): -2.127000 64.07100 ymin,ymax (A): 14.23300 76.43300 zmin,zma (A): -13.24800 34.34000 x,y,z range (A): 66.19800 62.20000 47.58800 scale (grids/A): 2.420013 object centre (A): 30.97200 45.33300 10.54600 number of atom coordinates read : 3576 total number of charged atoms : 3429 net assigned charge : -7.099989 assigned positive charge : 547.4420 centred at (gu) : 87.43681 78.31274 88.32088 assigned negative charge : -554.5439 centred at (gu) : 87.34193 78.42378 88.44309 start vw surface at 0.1400000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 172926 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30253 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 79729 mr = 126850 m= 22388 mr = 63600 m= 3661 mr = 16901 m= 259 mr = 2479 m= 2 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 6485 time to turn everything in is 1.480000 number of dielectric boundary points 69037 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 27386 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) : 1.613342 object centre at (A) : 30.97200 45.33300 10.54600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5910186E-03 -1.3498040E-02 midg,1,midg; midg,igrid,midg -0.4182947 -0.2773242 1,midg,midg; igrid,midg,midg 0.4172725 -7.8384653E-02 gauss-seidel spectral radius is 0.9991428 estimated iterations to convergence 270 setup time was (sec) 1.870000 now iterating at: 17:29:10 rms-change max change #iterations 9.482072 301.0585 at 10iterations 5.306422 120.7714 at 20iterations 2.957707 67.37134 at 30iterations 1.642158 39.06361 at 40iterations 0.9088732 18.51157 at 50iterations 0.5036452 11.34534 at 60iterations 0.2791703 5.235046 at 70iterations 0.1540611 3.258650 at 80iterations 8.4928043E-02 1.603477 at 90iterations 4.6825256E-02 0.8819275 at 100iterations 2.5841638E-02 0.4636197 at 110iterations 1.4244143E-02 0.2766829 at 120iterations 7.8588268E-03 0.1620255 at 130iterations 4.3365974E-03 8.3908081E-02 at 140iterations 2.3866699E-03 4.4399261E-02 at 150iterations 1.3154867E-03 2.7278304E-02 at 160iterations 7.2756549E-04 1.4839172E-02 at 170iterations 4.0390075E-04 7.6680183E-03 at 180iterations finished qdiffx linear iterations at : 17:29:25 total time elapsed so far: 17.82000 # loops : 180 mean,max change (kT/e) : 4.0390075E-04 7.6680183E-03 energy calculations done at 17.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.98000 DelPhi exited at 17:29:26 17.983u 0.467s 0:18.71 98.5% 0+0k 0+0io 0pf+0w