Sun Oct 9 04:09:49 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 Sun Oct 9 2011 at 04:09:49 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4836 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 has a net charge of 1.4000 !!! WARNING: FE 5 has a net charge of 1.4000 !!! WARNING: FE 6 has a net charge of 1.4000 !!! WARNING: FE 7 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.4213965 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): -2.133000 79.36700 ymin,ymax (A): -11.56100 55.76500 zmin,zma (A): -17.15800 67.32300 x,y,z range (A): 81.50001 67.32600 84.48100 scale (grids/A): 0.4213965 object centre (A): 38.61700 22.10200 25.08250 number of atom coordinates read : 4836 total number of charged atoms : 4517 net assigned charge : 20.80000 assigned positive charge : 708.7355 centred at (gu) : 85.25867 91.61589 83.92687 assigned negative charge : -687.9410 centred at (gu) : 85.10597 91.66276 83.83737 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5019 nv = 96 ne = 84 npr = 98653 no. pairs analyzed = 98653 no. exposed pairs = 6224 no. arc points = 44113 no. surface atoms = 2072 nbur = 2764 mkacc time = 0.2500000 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 = 1.988000 m= 124 mr = 2252 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 2891 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3250 ## 690 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 6673 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6729617E-12 7.1217966E-13 midg,1,midg; midg,igrid,midg 2.1499345E-12 2.4123036E-12 1,midg,midg; igrid,midg,midg -4.9723741E-12 1.3622953E-12 gauss-seidel spectral radius is 0.9713216 estimated iterations to convergence 49 setup time was (sec) 0.7500000 now iterating at: 04:09:50 rms-change max change #iterations 2.5796164E-02 10.47134 at 10iterations 3.0920135E-03 0.5100346 at 20iterations 1.0075121E-03 0.1881618 at 30iterations 3.4911997E-04 6.9856644E-02 at 40iterations 1.2315143E-04 2.5386810E-02 at 50iterations finished qdiffx linear iterations at : 04:09:54 total time elapsed so far: 4.790000 # loops : 50 mean,max change (kT/e) : 1.2315143E-04 2.5386810E-02 energy calculations done at 4.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.950000 DelPhi exited at 04:09:55 4.955u 0.408s 0:05.64 94.8% 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 Sun Oct 9 2011 at 04:09:55 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4836 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 has a net charge of 1.4000 !!! WARNING: FE 5 has a net charge of 1.4000 !!! WARNING: FE 6 has a net charge of 1.4000 !!! WARNING: FE 7 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.264189 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): -2.133000 79.36700 ymin,ymax (A): -11.56100 55.76500 zmin,zma (A): -17.15800 67.32300 x,y,z range (A): 81.50001 67.32600 84.48100 scale (grids/A): 1.264189 object centre (A): 38.61700 22.10200 25.08250 number of atom coordinates read : 4836 total number of charged atoms : 4517 net assigned charge : 20.80000 assigned positive charge : 708.7355 centred at (gu) : 75.77435 94.84600 71.77900 assigned negative charge : -687.9410 centred at (gu) : 75.31767 94.98810 71.51183 start vw surface at 0.1800000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 58826 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44113 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.848000 m= 12267 mr = 37475 m= 503 mr = 6939 m= 5 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 720 time to turn everything in is 0.5600000 number of dielectric boundary points 27090 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 689 ## 21 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 30976 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) : 0.4213965 object centre at (A) : 38.61700 22.10200 25.08250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3180057E-02 1.9654294E-03 midg,1,midg; midg,igrid,midg 2.9010151E-03 2.0533886E-03 1,midg,midg; igrid,midg,midg -8.3693606E-04 1.6528037E-03 gauss-seidel spectral radius is 0.9970112 estimated iterations to convergence 146 setup time was (sec) 0.8500000 now iterating at: 04:09:56 rms-change max change #iterations 2.288438 122.7462 at 10iterations 0.7438628 32.28446 at 20iterations 0.2426876 10.81910 at 30iterations 7.9466738E-02 3.389336 at 40iterations 2.6823483E-02 1.101611 at 50iterations 9.7705703E-03 0.4541626 at 60iterations 4.4496860E-03 0.1909142 at 70iterations 2.5415451E-03 0.1046410 at 80iterations 1.6518626E-03 6.7893982E-02 at 90iterations 1.1138967E-03 4.4193268E-02 at 100iterations 7.5904065E-04 2.9769897E-02 at 110iterations 5.1830849E-04 2.0141602E-02 at 120iterations finished qdiffx linear iterations at : 04:10:05 total time elapsed so far: 10.09000 # loops : 120 mean,max change (kT/e) : 5.1830849E-04 2.0141602E-02 energy calculations done at 10.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.27000 DelPhi exited at 04:10:06 10.273u 0.425s 0:11.12 96.1% 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 Sun Oct 9 2011 at 04:10:06 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4836 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 has a net charge of 1.4000 !!! WARNING: FE 5 has a net charge of 1.4000 !!! WARNING: FE 6 has a net charge of 1.4000 !!! WARNING: FE 7 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.896284 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): -2.133000 79.36700 ymin,ymax (A): -11.56100 55.76500 zmin,zma (A): -17.15800 67.32300 x,y,z range (A): 81.50001 67.32600 84.48100 scale (grids/A): 1.896284 object centre (A): 38.61700 22.10200 25.08250 number of atom coordinates read : 4836 total number of charged atoms : 4517 net assigned charge : 20.80000 assigned positive charge : 708.7355 centred at (gu) : 68.66107 97.26862 62.66807 assigned negative charge : -687.9410 centred at (gu) : 67.97649 97.48224 62.26767 start vw surface at 0.1600000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 138301 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44113 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 49057 mr = 94040 m= 7740 mr = 35277 m= 482 mr = 4794 m= 5 mr = 168 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 2392 time to turn everything in is 1.210000 number of dielectric boundary points 61306 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 198 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 35478 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) : 1.264189 object centre at (A) : 38.61700 22.10200 25.08250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4493827 2.6214805E-02 midg,1,midg; midg,igrid,midg 6.7694791E-02 3.0413082E-02 1,midg,midg; igrid,midg,midg -1.2737469E-02 2.1103853E-02 gauss-seidel spectral radius is 0.9987088 estimated iterations to convergence 220 setup time was (sec) 1.540000 now iterating at: 04:10:08 rms-change max change #iterations 7.022539 242.3779 at 10iterations 3.495047 103.5204 at 20iterations 1.724431 51.29768 at 30iterations 0.8429373 21.57479 at 40iterations 0.4123514 10.66971 at 50iterations 0.2007576 5.138700 at 60iterations 9.7355597E-02 2.362297 at 70iterations 4.7156319E-02 1.111641 at 80iterations 2.2957528E-02 0.5727673 at 90iterations 1.1167038E-02 0.3196965 at 100iterations 5.5350293E-03 0.1810026 at 110iterations 2.8023815E-03 7.4420929E-02 at 120iterations 1.5058380E-03 4.7039032E-02 at 130iterations 8.7816140E-04 2.8751373E-02 at 140iterations 5.6482089E-04 1.9611359E-02 at 150iterations 3.9305002E-04 1.2889862E-02 at 160iterations 2.8815342E-04 9.2124939E-03 at 170iterations 2.1581636E-04 6.6795349E-03 at 180iterations finished qdiffx linear iterations at : 04:10:23 total time elapsed so far: 17.09000 # loops : 180 mean,max change (kT/e) : 2.1581636E-04 6.6795349E-03 energy calculations done at 17.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.25000 DelPhi exited at 04:10:24 17.259u 0.472s 0:18.01 98.3% 0+0k 0+0io 0pf+0w