Sun Oct 9 15:25:10 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 15:25:10 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 = 5192 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: 0.4992008 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): 8.327001 63.77400 ymin,ymax (A): 53.51000 124.8240 zmin,zma (A): 32.26600 96.53900 x,y,z range (A): 55.44700 71.31400 64.27300 scale (grids/A): 0.4992008 object centre (A): 36.05050 89.16700 64.40250 number of atom coordinates read : 5192 total number of charged atoms : 5029 net assigned charge : 4.000029 assigned positive charge : 806.5240 centred at (gu) : 89.25496 90.24648 90.23826 assigned negative charge : -802.5306 centred at (gu) : 89.29065 90.18301 90.10046 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7828 nv = 96 ne = 84 npr = 105156 no. pairs analyzed = 105156 no. exposed pairs = 6387 no. arc points = 44089 no. surface atoms = 2143 nbur = 3049 mkacc time = 0.1700000 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= 254 mr = 4065 m= 0 mr = 8 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3400000 number of dielectric boundary points 4009 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4289 ## 733 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 10833 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0260479E-10 2.9022554E-10 midg,1,midg; midg,igrid,midg -7.5614522E-11 1.5385029E-10 1,midg,midg; igrid,midg,midg 1.1663816E-10 -2.5146779E-11 gauss-seidel spectral radius is 0.9795008 estimated iterations to convergence 58 setup time was (sec) 0.5500000 now iterating at: 15:25:10 rms-change max change #iterations 6.2296432E-02 11.38992 at 10iterations 3.8081820E-03 0.5754423 at 20iterations 6.7561510E-04 9.3725681E-02 at 30iterations 2.3075004E-04 3.7361145E-02 at 40iterations 8.2032035E-05 1.4482498E-02 at 50iterations finished qdiffx linear iterations at : 15:25:13 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 8.2032035E-05 1.4482498E-02 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 15:25:14 3.608u 0.179s 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 15:25:14 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 = 5192 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: 1.497602 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): 8.327001 63.77400 ymin,ymax (A): 53.51000 124.8240 zmin,zma (A): 32.26600 96.53900 x,y,z range (A): 55.44700 71.31400 64.27300 scale (grids/A): 1.497602 object centre (A): 36.05050 89.16700 64.40250 number of atom coordinates read : 5192 total number of charged atoms : 5029 net assigned charge : 4.000029 assigned positive charge : 806.5240 centred at (gu) : 87.76330 90.73794 90.71301 assigned negative charge : -802.5306 centred at (gu) : 87.87138 90.54872 90.30123 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 89289 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44089 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 24915 mr = 61176 m= 1880 mr = 16411 m= 34 mr = 798 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1909 time to turn everything in is 0.4300000 number of dielectric boundary points 37733 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 703 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 37489 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) : 0.4992008 object centre at (A) : 36.05050 89.16700 64.40250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8699728E-03 1.4184197E-02 midg,1,midg; midg,igrid,midg -5.5748802E-03 1.5673293E-02 1,midg,midg; igrid,midg,midg 2.7924115E-03 7.5992133E-04 gauss-seidel spectral radius is 0.9980417 estimated iterations to convergence 180 setup time was (sec) 0.6600000 now iterating at: 15:25:15 rms-change max change #iterations 3.827501 147.0996 at 10iterations 1.540713 54.96363 at 20iterations 0.6215250 21.22152 at 30iterations 0.2495558 8.196856 at 40iterations 0.1010232 3.180567 at 50iterations 4.1014072E-02 1.601830 at 60iterations 1.6598484E-02 0.5151329 at 70iterations 6.7772279E-03 0.2616129 at 80iterations 2.8072065E-03 9.9801064E-02 at 90iterations 1.2114544E-03 3.5133362E-02 at 100iterations 5.6481618E-04 1.8547058E-02 at 110iterations 2.9811909E-04 1.0828018E-02 at 120iterations finished qdiffx linear iterations at : 15:25:22 total time elapsed so far: 7.910000 # loops : 120 mean,max change (kT/e) : 2.9811909E-04 1.0828018E-02 energy calculations done at 7.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.050000 DelPhi exited at 15:25:22 8.051u 0.208s 0:08.53 96.7% 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 15:25:22 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 = 5192 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: 2.246403 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): 8.327001 63.77400 ymin,ymax (A): 53.51000 124.8240 zmin,zma (A): 32.26600 96.53900 x,y,z range (A): 55.44700 71.31400 64.27300 scale (grids/A): 2.246403 object centre (A): 36.05050 89.16700 64.40250 number of atom coordinates read : 5192 total number of charged atoms : 5029 net assigned charge : 4.000029 assigned positive charge : 806.5240 centred at (gu) : 86.64460 91.10662 91.06923 assigned negative charge : -802.5306 centred at (gu) : 86.80698 90.82294 90.45154 start vw surface at 0.1300000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 208782 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44089 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 90173 mr = 150995 m= 21574 mr = 69938 m= 2658 mr = 15513 m= 101 mr = 1580 m= 0 mr = 20 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 6562 time to turn everything in is 1.050000 number of dielectric boundary points 85242 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 40095 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) : 1.497602 object centre at (A) : 36.05050 89.16700 64.40250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.3203480E-02 0.2439870 midg,1,midg; midg,igrid,midg -0.2112235 0.2107522 1,midg,midg; igrid,midg,midg 5.5686992E-02 2.7654622E-02 gauss-seidel spectral radius is 0.9991460 estimated iterations to convergence 270 setup time was (sec) 1.300000 now iterating at: 15:25:24 rms-change max change #iterations 10.53659 300.9862 at 10iterations 5.981266 160.1895 at 20iterations 3.384844 74.76933 at 30iterations 1.902513 45.51366 at 40iterations 1.066743 23.72143 at 50iterations 0.5950214 12.92714 at 60iterations 0.3314424 6.405026 at 70iterations 0.1846242 3.597679 at 80iterations 0.1022890 2.102575 at 90iterations 5.6677878E-02 1.049968 at 100iterations 3.1383883E-02 0.5942688 at 110iterations 1.7405901E-02 0.3902359 at 120iterations 9.6151661E-03 0.2007732 at 130iterations 5.3166202E-03 0.1036464 at 140iterations 2.9391753E-03 6.9824219E-02 at 150iterations 1.6303058E-03 3.0847549E-02 at 160iterations 8.9877669E-04 1.7173767E-02 at 170iterations 4.9906981E-04 9.2802048E-03 at 180iterations finished qdiffx linear iterations at : 15:25:35 total time elapsed so far: 12.95000 # loops : 180 mean,max change (kT/e) : 4.9906981E-04 9.2802048E-03 energy calculations done at 12.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.08000 DelPhi exited at 15:25:36 13.085u 0.210s 0:13.62 97.5% 0+0k 0+0io 0pf+0w