Mon Oct 10 14:15:17 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 Mon Oct 10 2011 at 14:15:17 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 = 3853 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: 0.5110023 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): -38.32700 27.55700 ymin,ymax (A): -23.15200 46.51500 zmin,zma (A): -77.02400 -7.667000 x,y,z range (A): 65.88400 69.66701 69.35700 scale (grids/A): 0.5110023 object centre (A): -5.385000 11.68150 -42.34550 number of atom coordinates read : 3853 total number of charged atoms : 3684 net assigned charge : -9.999972 assigned positive charge : 575.9396 centred at (gu) : 90.43054 86.95946 90.85581 assigned negative charge : -585.9421 centred at (gu) : 90.49126 86.86040 90.88482 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6620 nv = 96 ne = 84 npr = 72904 no. pairs analyzed = 72904 no. exposed pairs = 5732 no. arc points = 41569 no. surface atoms = 1892 nbur = 1961 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 = 1.680000 m= 226 mr = 2844 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3998 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4004 ## 619 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8803 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.8740061E-11 -2.4495858E-10 midg,1,midg; midg,igrid,midg -7.8534862E-10 3.1336257E-11 1,midg,midg; igrid,midg,midg -5.5541891E-12 -2.9605213E-10 gauss-seidel spectral radius is 0.9803733 estimated iterations to convergence 59 setup time was (sec) 0.7100000 now iterating at: 14:15:18 rms-change max change #iterations 5.7876579E-02 10.47285 at 10iterations 3.1785511E-03 0.5748444 at 20iterations 1.9346492E-04 3.0593872E-02 at 30iterations 1.8490429E-05 3.5833120E-03 at 40iterations 3.5209773E-06 8.2761049E-04 at 50iterations finished qdiffx linear iterations at : 14:15:22 total time elapsed so far: 4.470000 # loops : 50 mean,max change (kT/e) : 3.5209773E-06 8.2761049E-04 energy calculations done at 4.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.640000 DelPhi exited at 14:15:22 4.646u 0.434s 0:05.46 92.8% 0+0k 0+0io 6pf+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 Mon Oct 10 2011 at 14:15:23 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 = 3853 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: 1.533007 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): -38.32700 27.55700 ymin,ymax (A): -23.15200 46.51500 zmin,zma (A): -77.02400 -7.667000 x,y,z range (A): 65.88400 69.66701 69.35700 scale (grids/A): 1.533007 object centre (A): -5.385000 11.68150 -42.34550 number of atom coordinates read : 3853 total number of charged atoms : 3684 net assigned charge : -9.999972 assigned positive charge : 575.9396 centred at (gu) : 91.29037 80.87746 92.56654 assigned negative charge : -585.9421 centred at (gu) : 91.47352 80.58098 92.65419 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 73395 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41569 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 19225 mr = 44662 m= 1544 mr = 11478 m= 36 mr = 496 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 149 time to turn everything in is 0.6400000 number of dielectric boundary points 37565 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 554 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 27669 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) : 0.5110023 object centre at (A) : -5.385000 11.68150 -42.34550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1380263E-02 -7.7314754E-03 midg,1,midg; midg,igrid,midg -1.4827277E-02 2.2260919E-03 1,midg,midg; igrid,midg,midg -2.2514637E-03 -4.9321488E-03 gauss-seidel spectral radius is 0.9980388 estimated iterations to convergence 180 setup time was (sec) 0.9400000 now iterating at: 14:15:24 rms-change max change #iterations 3.323901 149.6140 at 10iterations 1.324604 50.26191 at 20iterations 0.5298520 20.75140 at 30iterations 0.2124802 7.991385 at 40iterations 8.5166305E-02 3.187648 at 50iterations 3.4289122E-02 1.230646 at 60iterations 1.3768010E-02 0.4876003 at 70iterations 5.5310149E-03 0.2022972 at 80iterations 2.2299956E-03 8.7158203E-02 at 90iterations 8.9681556E-04 3.0162811E-02 at 100iterations 3.5973202E-04 1.2878418E-02 at 110iterations 1.4622993E-04 5.0897598E-03 at 120iterations finished qdiffx linear iterations at : 14:15:33 total time elapsed so far: 10.39000 # loops : 120 mean,max change (kT/e) : 1.4622993E-04 5.0897598E-03 energy calculations done at 10.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.56000 DelPhi exited at 14:15:34 10.569u 0.462s 0:11.37 96.9% 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 Mon Oct 10 2011 at 14:15:34 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 = 3853 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: 2.299510 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): -38.32700 27.55700 ymin,ymax (A): -23.15200 46.51500 zmin,zma (A): -77.02400 -7.667000 x,y,z range (A): 65.88400 69.66701 69.35700 scale (grids/A): 2.299510 object centre (A): -5.385000 11.68150 -42.34550 number of atom coordinates read : 3853 total number of charged atoms : 3684 net assigned charge : -9.999972 assigned positive charge : 575.9396 centred at (gu) : 91.93533 76.31590 93.84956 assigned negative charge : -585.9421 centred at (gu) : 92.21030 75.87145 93.98125 start vw surface at 0.1500000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 170527 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41569 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 68931 mr = 111377 m= 16376 mr = 50112 m= 2056 mr = 10690 m= 105 mr = 1010 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 511 time to turn everything in is 1.510000 number of dielectric boundary points 84784 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 58 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 29396 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) : 1.533007 object centre at (A) : -5.385000 11.68150 -42.34550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2153240 -0.1191711 midg,1,midg; midg,igrid,midg -9.7498916E-02 6.4661860E-02 1,midg,midg; igrid,midg,midg -6.0427010E-02 -7.6496661E-02 gauss-seidel spectral radius is 0.9991106 estimated iterations to convergence 265 setup time was (sec) 1.860000 now iterating at: 14:15:36 rms-change max change #iterations 9.200894 285.3270 at 10iterations 5.203243 139.2714 at 20iterations 2.916734 68.59440 at 30iterations 1.619801 36.25966 at 40iterations 0.8943494 19.21048 at 50iterations 0.4940379 10.72342 at 60iterations 0.2723633 5.680235 at 70iterations 0.1491251 3.164145 at 80iterations 8.1556156E-02 1.642981 at 90iterations 4.4577606E-02 0.9598808 at 100iterations 2.4382712E-02 0.5169487 at 110iterations 1.3285922E-02 0.3060474 at 120iterations 7.2617633E-03 0.1531506 at 130iterations 3.9491197E-03 7.8504562E-02 at 140iterations 2.1533680E-03 4.8008204E-02 at 150iterations 1.1722925E-03 2.4491787E-02 at 160iterations 6.3927134E-04 1.3198853E-02 at 170iterations 3.4774712E-04 6.9694519E-03 at 180iterations finished qdiffx linear iterations at : 14:15:52 total time elapsed so far: 17.89000 # loops : 180 mean,max change (kT/e) : 3.4774712E-04 6.9694519E-03 energy calculations done at 17.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.06000 DelPhi exited at 14:15:53 18.063u 0.466s 0:19.43 95.3% 0+0k 0+0io 0pf+0w