Tue Oct 11 03:15:18 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 Tue Oct 11 2011 at 03:15:19 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2112 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6969050 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): -34.60000 11.64400 ymin,ymax (A): -16.34500 28.04400 zmin,zma (A): -26.51900 24.56400 x,y,z range (A): 46.24400 44.38900 51.08300 scale (grids/A): 0.6969050 object centre (A): -11.47800 5.849501 -0.9775009 number of atom coordinates read : 2112 total number of charged atoms : 2002 net assigned charge : 3.000008 assigned positive charge : 316.3515 centred at (gu) : 89.48750 90.80193 89.23997 assigned negative charge : -313.3519 centred at (gu) : 89.48613 90.80925 89.02492 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7080 nv = 96 ne = 84 npr = 43199 no. pairs analyzed = 43199 no. exposed pairs = 2703 no. arc points = 18797 no. surface atoms = 909 nbur = 1203 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 421 mr = 3943 m= 3 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3501 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1698 ## 157 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 7892 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.6538718E-08 8.8270887E-08 midg,1,midg; midg,igrid,midg 2.0017007E-08 2.0518540E-08 1,midg,midg; igrid,midg,midg 2.1998705E-08 1.9060018E-08 gauss-seidel spectral radius is 0.9892808 estimated iterations to convergence 79 setup time was (sec) 0.5200000 now iterating at: 03:15:19 rms-change max change #iterations 0.1964575 26.09176 at 10iterations 2.3222968E-02 3.457379 at 20iterations 2.8384277E-03 0.4022064 at 30iterations 3.6998573E-04 5.0422668E-02 at 40iterations 6.4856264E-05 1.0935783E-02 at 50iterations finished qdiffx linear iterations at : 03:15:24 total time elapsed so far: 4.760000 # loops : 50 mean,max change (kT/e) : 6.4856264E-05 1.0935783E-02 energy calculations done at 4.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.920000 DelPhi exited at 03:15:24 4.924u 0.455s 0:05.89 91.1% 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 Tue Oct 11 2011 at 03:15:24 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2112 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.090715 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): -34.60000 11.64400 ymin,ymax (A): -16.34500 28.04400 zmin,zma (A): -26.51900 24.56400 x,y,z range (A): 46.24400 44.38900 51.08300 scale (grids/A): 2.090715 object centre (A): -11.47800 5.849501 -0.9775009 number of atom coordinates read : 2112 total number of charged atoms : 2002 net assigned charge : 3.000008 assigned positive charge : 316.3515 centred at (gu) : 88.46233 92.40536 87.71949 assigned negative charge : -313.3519 centred at (gu) : 88.45828 92.42773 87.07486 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 75167 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18797 grid for indexing accessible points = 1.400000 m= 28016 mr = 52320 m= 5376 mr = 20760 m= 473 mr = 3437 m= 10 mr = 197 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 0.6300000 number of dielectric boundary points 32328 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 75 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 15890 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) : 0.6969050 object centre at (A) : -11.47800 5.849501 -0.9775009 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.1564881E-02 7.0653662E-02 midg,1,midg; midg,igrid,midg 1.3184307E-02 -9.4134333E-03 1,midg,midg; igrid,midg,midg -3.4384329E-02 9.7801453E-03 gauss-seidel spectral radius is 0.9988117 estimated iterations to convergence 230 setup time was (sec) 0.9700000 now iterating at: 03:15:26 rms-change max change #iterations 4.566387 193.1506 at 10iterations 2.238889 74.46088 at 20iterations 1.114181 33.93254 at 30iterations 0.5477322 16.34085 at 40iterations 0.2702793 10.20187 at 50iterations 0.1335790 4.218498 at 60iterations 6.5714173E-02 1.860558 at 70iterations 3.2540791E-02 1.044259 at 80iterations 1.6040960E-02 0.4698095 at 90iterations 7.9314187E-03 0.2236018 at 100iterations 3.9107320E-03 0.1192093 at 110iterations 1.9342321E-03 5.8963776E-02 at 120iterations finished qdiffx linear iterations at : 03:15:37 total time elapsed so far: 11.96000 # loops : 120 mean,max change (kT/e) : 1.9342321E-03 5.8963776E-02 energy calculations done at 11.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.12000 DelPhi exited at 03:15:37 12.125u 0.485s 0:13.02 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 Tue Oct 11 2011 at 03:15:37 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2112 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.136073 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): -34.60000 11.64400 ymin,ymax (A): -16.34500 28.04400 zmin,zma (A): -26.51900 24.56400 x,y,z range (A): 46.24400 44.38900 51.08300 scale (grids/A): 3.136073 object centre (A): -11.47800 5.849501 -0.9775009 number of atom coordinates read : 2112 total number of charged atoms : 2002 net assigned charge : 3.000008 assigned positive charge : 316.3515 centred at (gu) : 87.69334 93.60801 86.57919 assigned negative charge : -313.3519 centred at (gu) : 87.68751 93.64170 85.61224 start vw surface at 0.1100000 fill in re-entrant regions at 0.7800000 boundary points on vw surface= 174054 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18797 grid for indexing accessible points = 1.400000 m= 88449 mr = 126931 m= 34881 mr = 72579 m= 9952 mr = 28061 m= 1873 mr = 7581 m= 186 mr = 1264 m= 12 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.940000 number of dielectric boundary points 72895 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.090000 number of grid points assigned charge 16016 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) : 2.090715 object centre at (A) : -11.47800 5.849501 -0.9775009 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7577231 0.5520619 midg,1,midg; midg,igrid,midg 0.1022258 -0.1225892 1,midg,midg; igrid,midg,midg -0.3461752 0.1150293 gauss-seidel spectral radius is 0.9993042 estimated iterations to convergence 299 setup time was (sec) 2.320000 now iterating at: 03:15:40 rms-change max change #iterations 10.24953 402.5827 at 10iterations 6.038758 143.1312 at 20iterations 3.565377 78.63750 at 30iterations 2.096070 54.23993 at 40iterations 1.230403 22.52484 at 50iterations 0.7220306 12.52571 at 60iterations 0.4240515 8.716072 at 70iterations 0.2480028 4.306459 at 80iterations 0.1449245 2.581500 at 90iterations 8.5022472E-02 1.472931 at 100iterations 4.9753796E-02 0.8520508 at 110iterations 2.9015463E-02 0.4777026 at 120iterations 1.6994948E-02 0.2879877 at 130iterations 9.9127358E-03 0.1688282 at 140iterations 5.8106720E-03 0.1011238 at 150iterations 3.3917304E-03 5.7387352E-02 at 160iterations 1.9845958E-03 3.5006523E-02 at 170iterations 1.1672324E-03 1.9432068E-02 at 180iterations finished qdiffx linear iterations at : 03:15:59 total time elapsed so far: 21.26000 # loops : 180 mean,max change (kT/e) : 1.1672324E-03 1.9432068E-02 energy calculations done at 21.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.43000 DelPhi exited at 03:16:00 21.434u 0.510s 0:22.28 98.4% 0+0k 0+0io 0pf+0w