Thu Jan 19 13:31:25 PST 2012 #!/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 Thu Jan 19 2012 at 13:31:30 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: 25 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.0000000E+00 grid size : 179 scale,in grids/A, set to be: 9.368422 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): -1.900000 1.900000 ymin,ymax (A): -1.900000 1.900000 zmin,zma (A): -1.900000 1.900000 x,y,z range (A): 3.800000 3.800000 3.800000 scale (grids/A): 9.368422 object centre (A): 0.0000000E+00 0.0000000E+00 0.0000000E+00 number of atom coordinates read : 1 total number of charged atoms : 0 net assigned charge : 0.0000000E+00 assigned positive charge : 0.0000000E+00 centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 assigned negative charge : 0.0000000E+00 centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 start vw surface at 3.9999999E-02 fill in re-entrant regions at 3.9999999E-02 boundary points on vw surface= 3318 nv = 96 ne = 84 npr = 0 no. pairs analyzed = 0 no. exposed pairs = 0 no. arc points = 0 no. surface atoms = 1 nbur = 0 mkacc time = 0.0000000E+00 grid for indexing accessible points = 1.400000 m= 0 mr = 0 time to grow re-entrant surface = 0.0000000E+00 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 5.0000001E-02 number of dielectric boundary points 3318 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.1200000 number of grid points assigned charge 0 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 0.0000000E+00 0.0000000E+00 midg,1,midg; midg,igrid,midg 0.0000000E+00 0.0000000E+00 1,midg,midg; igrid,midg,midg 0.0000000E+00 0.0000000E+00 gauss-seidel spectral radius is 0.9996225 estimated iterations to convergence 405 setup time was (sec) 0.2400000 now iterating at: 13:31:32 rms-change max change #iterations 0.0000000E+00 0.0000000E+00 at 10iterations finished qdiffx linear iterations at : 13:31:34 total time elapsed so far: 0.9400000 # loops : 10 mean,max change (kT/e) : 0.0000000E+00 0.0000000E+00 energy calculations done at 0.9400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 1.080000 DelPhi exited at 13:31:36 1.084u 0.181s 0:06.69 18.8% 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 Thu Jan 19 2012 at 13:31:38 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: 25 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.0000000E+00 grid size : 179 scale,in grids/A, set to be: 28.10526 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): -1.900000 1.900000 ymin,ymax (A): -1.900000 1.900000 zmin,zma (A): -1.900000 1.900000 x,y,z range (A): 3.800000 3.800000 3.800000 scale (grids/A): 28.10526 object centre (A): 0.0000000E+00 0.0000000E+00 0.0000000E+00 number of atom coordinates read : 1 total number of charged atoms : 0 net assigned charge : 0.0000000E+00 assigned positive charge : 0.0000000E+00 centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 assigned negative charge : 0.0000000E+00 centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 start vw surface at 2.9999999E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 29730 nv = 96 ne = 84 npr = 0 no. pairs analyzed = 0 no. exposed pairs = 0 no. arc points = 0 no. surface atoms = 1 nbur = 0 mkacc time = 0.0000000E+00 grid for indexing accessible points = 1.400000 m= 0 mr = 0 time to grow re-entrant surface = 3.0000001E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 29730 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 0 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) : 9.368422 object centre at (A) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.0000000E+00 0.0000000E+00 midg,1,midg; midg,igrid,midg 0.0000000E+00 0.0000000E+00 1,midg,midg; igrid,midg,midg 0.0000000E+00 0.0000000E+00 gauss-seidel spectral radius is 0.9994026 estimated iterations to convergence 323 setup time was (sec) 0.4000000 now iterating at: 13:31:41 rms-change max change #iterations 0.0000000E+00 0.0000000E+00 at 10iterations finished qdiffx linear iterations at : 13:31:43 total time elapsed so far: 1.150000 # loops : 10 mean,max change (kT/e) : 0.0000000E+00 0.0000000E+00 energy calculations done at 1.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 1.300000 DelPhi exited at 13:31:46 1.299u 0.222s 0:08.56 17.6% 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 Thu Jan 19 2012 at 13:31:47 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: 25 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.0000000E+00 grid size : 179 scale,in grids/A, set to be: 42.15789 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): -1.900000 1.900000 ymin,ymax (A): -1.900000 1.900000 zmin,zma (A): -1.900000 1.900000 x,y,z range (A): 3.800000 3.800000 3.800000 scale (grids/A): 42.15789 object centre (A): 0.0000000E+00 0.0000000E+00 0.0000000E+00 number of atom coordinates read : 1 total number of charged atoms : 0 net assigned charge : 0.0000000E+00 assigned positive charge : 0.0000000E+00 centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 assigned negative charge : 0.0000000E+00 centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 start vw surface at 3.9999999E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 67038 nv = 96 ne = 84 npr = 0 no. pairs analyzed = 0 no. exposed pairs = 0 no. arc points = 0 no. surface atoms = 1 nbur = 0 mkacc time = 0.0000000E+00 grid for indexing accessible points = 1.400000 m= 0 mr = 0 time to grow re-entrant surface = 6.0000017E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 67038 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 0 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) : 28.10526 object centre at (A) : 0.0000000E+00 0.0000000E+00Segmentation fault 1.292u 0.195s 0:06.60 22.4% 0+0k 0+0io 0pf+0w