Sun Oct 9 16:41:51 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+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 16:41:51 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2995 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: 0.5196852 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): 23.84600 81.42900 ymin,ymax (A): -24.43200 26.78300 zmin,zma (A): -37.91900 30.58400 x,y,z range (A): 57.58300 51.21500 68.50301 scale (grids/A): 0.5196852 object centre (A): 52.63750 1.175500 -3.667501 number of atom coordinates read : 2995 total number of charged atoms : 2852 net assigned charge : -0.9999954 assigned positive charge : 445.1579 centred at (gu) : 90.17183 88.71788 90.90986 assigned negative charge : -446.1595 centred at (gu) : 90.21635 88.78925 90.86713 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5088 nv = 96 ne = 84 npr = 59912 no. pairs analyzed = 59912 no. exposed pairs = 4190 no. arc points = 29450 no. surface atoms = 1391 nbur = 1604 mkacc time = 0.1300000 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 = 1.624000 m= 187 mr = 2301 m= 0 mr = 8 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 2966 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2931 ## 438 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 6900 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.9487710E-11 9.7467749E-11 midg,1,midg; midg,igrid,midg 2.0168034E-10 -1.3961918E-10 1,midg,midg; igrid,midg,midg 7.6972630E-11 -1.3634213E-10 gauss-seidel spectral radius is 0.9809380 estimated iterations to convergence 60 setup time was (sec) 0.5200000 now iterating at: 16:41:52 rms-change max change #iterations 5.6054380E-02 11.90449 at 10iterations 3.3016810E-03 0.5458336 at 20iterations 2.3835110E-04 4.0918350E-02 at 30iterations 4.4723929E-05 9.2592239E-03 at 40iterations 1.2849091E-05 2.7446747E-03 at 50iterations finished qdiffx linear iterations at : 16:41:54 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 1.2849091E-05 2.7446747E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 16:41:55 3.100u 0.130s 0:03.54 91.2% 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 16:41:55 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 = 2995 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: 1.559056 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): 23.84600 81.42900 ymin,ymax (A): -24.43200 26.78300 zmin,zma (A): -37.91900 30.58400 x,y,z range (A): 57.58300 51.21500 68.50301 scale (grids/A): 1.559056 object centre (A): 52.63750 1.175500 -3.667501 number of atom coordinates read : 2995 total number of charged atoms : 2852 net assigned charge : -0.9999954 assigned positive charge : 445.1579 centred at (gu) : 90.51478 86.15237 92.72892 assigned negative charge : -446.1595 centred at (gu) : 90.64841 86.36771 92.60149 start vw surface at 0.1600000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 56312 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29450 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 16128 mr = 35497 m= 1655 mr = 10169 m= 35 mr = 707 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 255 time to turn everything in is 0.4200000 number of dielectric boundary points 27758 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 405 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 21524 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) : 0.5196852 object centre at (A) : 52.63750 1.175500 -3.667501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0233429E-02 -3.8313953E-04 midg,1,midg; midg,igrid,midg 4.2538834E-03 -4.9138558E-03 1,midg,midg; igrid,midg,midg -1.2671729E-03 -1.0680815E-03 gauss-seidel spectral radius is 0.9980114 estimated iterations to convergence 178 setup time was (sec) 0.6700000 now iterating at: 16:41:55 rms-change max change #iterations 3.011012 140.2213 at 10iterations 1.201291 50.90063 at 20iterations 0.4788169 18.87405 at 30iterations 0.1905123 7.325620 at 40iterations 7.6694623E-02 3.007260 at 50iterations 3.0676927E-02 1.314091 at 60iterations 1.2183934E-02 0.4614449 at 70iterations 4.9155750E-03 0.1873474 at 80iterations 1.9796074E-03 8.0884933E-02 at 90iterations 7.9918269E-04 3.3054352E-02 at 100iterations 3.2801222E-04 1.3216972E-02 at 110iterations 1.4037846E-04 5.6319237E-03 at 120iterations finished qdiffx linear iterations at : 16:42:02 total time elapsed so far: 6.850000 # loops : 120 mean,max change (kT/e) : 1.4037846E-04 5.6319237E-03 energy calculations done at 6.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.050000 DelPhi exited at 16:42:02 7.050u 0.179s 0:07.55 95.6% 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 16:42:02 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 = 2995 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: 2.338583 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): 23.84600 81.42900 ymin,ymax (A): -24.43200 26.78300 zmin,zma (A): -37.91900 30.58400 x,y,z range (A): 57.58300 51.21500 68.50301 scale (grids/A): 2.338583 object centre (A): 52.63750 1.175500 -3.667501 number of atom coordinates read : 2995 total number of charged atoms : 2852 net assigned charge : -0.9999954 assigned positive charge : 445.1579 centred at (gu) : 90.77177 84.22835 94.09336 assigned negative charge : -446.1595 centred at (gu) : 90.97266 84.55149 93.90219 start vw surface at 0.1600000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 130819 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29450 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 55584 mr = 87972 m= 15543 mr = 41350 m= 2374 mr = 11035 m= 131 mr = 1431 m= 5 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 694 time to turn everything in is 0.9500000 number of dielectric boundary points 62644 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 31 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 22747 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) : 1.559056 object centre at (A) : 52.63750 1.175500 -3.667501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4195256 2.3222862E-02 midg,1,midg; midg,igrid,midg 0.1056213 -8.4534466E-02 1,midg,midg; igrid,midg,midg -5.1620807E-02 -2.9256786E-03 gauss-seidel spectral radius is 0.9990861 estimated iterations to convergence 261 setup time was (sec) 1.220000 now iterating at: 16:42:04 rms-change max change #iterations 8.104046 283.1400 at 10iterations 4.508989 121.4547 at 20iterations 2.486711 64.46144 at 30iterations 1.367604 35.72296 at 40iterations 0.7483333 18.03867 at 50iterations 0.4086483 9.885668 at 60iterations 0.2224875 6.627065 at 70iterations 0.1209624 3.076826 at 80iterations 6.5578610E-02 1.639118 at 90iterations 3.5475008E-02 0.7872734 at 100iterations 1.9266788E-02 0.5123994 at 110iterations 1.0398848E-02 0.2355161 at 120iterations 5.6433766E-03 0.1357536 at 130iterations 3.0414597E-03 6.4504981E-02 at 140iterations 1.6454663E-03 3.6475182E-02 at 150iterations 8.8973070E-04 1.9160271E-02 at 160iterations 4.7944047E-04 1.0646820E-02 at 170iterations 2.5930133E-04 5.7258606E-03 at 180iterations finished qdiffx linear iterations at : 16:42:13 total time elapsed so far: 10.87000 # loops : 180 mean,max change (kT/e) : 2.5930133E-04 5.7258606E-03 energy calculations done at 10.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.09000 DelPhi exited at 16:42:14 11.095u 0.189s 0:11.54 97.6% 0+0k 0+0io 0pf+0w