Sat Oct 8 19:49:18 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+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 Sat Oct 8 2011 at 19:49:18 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2410 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 522 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6602007 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): -30.72800 17.71400 ymin,ymax (A): -24.24500 23.20000 zmin,zma (A): -12.09600 41.82700 x,y,z range (A): 48.44200 47.44500 53.92300 scale (grids/A): 0.6602007 object centre (A): -6.507000 -0.5225000 14.86550 number of atom coordinates read : 2410 total number of charged atoms : 2271 net assigned charge : 2.500008 assigned positive charge : 361.3264 centred at (gu) : 88.74935 89.29109 89.68458 assigned negative charge : -358.8268 centred at (gu) : 88.62695 89.35161 89.63493 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6899 nv = 96 ne = 84 npr = 51142 no. pairs analyzed = 51142 no. exposed pairs = 2767 no. arc points = 19870 no. surface atoms = 921 nbur = 1489 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 403 mr = 3982 m= 0 mr = 59 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 218 time to turn everything in is 0.3300000 number of dielectric boundary points 3261 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1858 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8218 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7000806E-09 1.4725642E-08 midg,1,midg; midg,igrid,midg 2.0514248E-08 -3.8417789E-09 1,midg,midg; igrid,midg,midg -2.1166089E-08 2.2223537E-08 gauss-seidel spectral radius is 0.9880873 estimated iterations to convergence 75 setup time was (sec) 0.6100000 now iterating at: 19:49:19 rms-change max change #iterations 0.1611734 22.11757 at 10iterations 1.7191604E-02 2.272320 at 20iterations 1.8326627E-03 0.2844677 at 30iterations 1.9846276E-04 2.7450562E-02 at 40iterations 2.0992969E-05 2.6540756E-03 at 50iterations finished qdiffx linear iterations at : 19:49:22 total time elapsed so far: 3.880000 # loops : 50 mean,max change (kT/e) : 2.0992969E-05 2.6540756E-03 energy calculations done at 3.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.050000 DelPhi exited at 19:49:22 4.055u 0.262s 0:04.57 94.3% 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 Sat Oct 8 2011 at 19:49:22 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2410 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 522 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.980602 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): -30.72800 17.71400 ymin,ymax (A): -24.24500 23.20000 zmin,zma (A): -12.09600 41.82700 x,y,z range (A): 48.44200 47.44500 53.92300 scale (grids/A): 1.980602 object centre (A): -6.507000 -0.5225000 14.86550 number of atom coordinates read : 2410 total number of charged atoms : 2271 net assigned charge : 2.500008 assigned positive charge : 361.3264 centred at (gu) : 86.24753 87.87312 89.05334 assigned negative charge : -358.8268 centred at (gu) : 85.88069 88.05460 88.90483 start vw surface at 0.1500000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 74310 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19870 grid for indexing accessible points = 1.400000 m= 27569 mr = 52492 m= 4834 mr = 20808 m= 361 mr = 3314 m= 3 mr = 157 m= 0 mr = 2 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 5427 time to turn everything in is 0.6700000 number of dielectric boundary points 30304 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 113 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 17952 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) : 0.6602007 object centre at (A) : -6.507000 -0.5225000 14.86550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2861989E-02 -1.1103564E-02 midg,1,midg; midg,igrid,midg 1.6979955E-02 7.8812698E-03 1,midg,midg; igrid,midg,midg 8.8934209E-03 5.7501469E-02 gauss-seidel spectral radius is 0.9987091 estimated iterations to convergence 220 setup time was (sec) 0.9600000 now iterating at: 19:49:24 rms-change max change #iterations 4.352827 182.9505 at 10iterations 2.081134 65.67841 at 20iterations 0.9947698 32.13308 at 30iterations 0.4771688 15.08238 at 40iterations 0.2284041 7.967751 at 50iterations 0.1091459 3.413834 at 60iterations 5.2399255E-02 1.747490 at 70iterations 2.5044383E-02 0.7459526 at 80iterations 1.1977051E-02 0.3938293 at 90iterations 5.7195248E-03 0.1997623 at 100iterations 2.7411233E-03 9.0499878E-02 at 110iterations 1.3144340E-03 4.2467117E-02 at 120iterations finished qdiffx linear iterations at : 19:49:32 total time elapsed so far: 9.210000 # loops : 120 mean,max change (kT/e) : 1.3144340E-03 4.2467117E-02 energy calculations done at 9.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.390000 DelPhi exited at 19:49:32 9.395u 0.296s 0:09.98 96.9% 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 Sat Oct 8 2011 at 19:49:32 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2410 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 522 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.970903 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): -30.72800 17.71400 ymin,ymax (A): -24.24500 23.20000 zmin,zma (A): -12.09600 41.82700 x,y,z range (A): 48.44200 47.44500 53.92300 scale (grids/A): 2.970903 object centre (A): -6.507000 -0.5225000 14.86550 number of atom coordinates read : 2410 total number of charged atoms : 2271 net assigned charge : 2.500008 assigned positive charge : 361.3264 centred at (gu) : 84.37128 86.80962 88.57981 assigned negative charge : -358.8268 centred at (gu) : 83.82102 87.08197 88.35731 start vw surface at 0.1500000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 171848 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19870 grid for indexing accessible points = 1.400000 m= 88402 mr = 126800 m= 33280 mr = 73549 m= 9015 mr = 27370 m= 1508 mr = 7036 m= 118 mr = 1094 m= 2 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 18811 time to turn everything in is 1.710000 number of dielectric boundary points 68262 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.860000 number of grid points assigned charge 18168 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) : 1.980602 object centre at (A) : -6.507000 -0.5225000 14.86550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1050585 -0.1380498 midg,1,midg; midg,igrid,midg 0.1838408 8.0170117E-02 1,midg,midg; igrid,midg,midg 0.1530033 0.6462613 gauss-seidel spectral radius is 0.9992672 estimated iterations to convergence 292 setup time was (sec) 2.030000 now iterating at: 19:49:35 rms-change max change #iterations 9.942399 469.9005 at 10iterations 5.735717 155.6611 at 20iterations 3.314902 64.22148 at 30iterations 1.916586 36.77164 at 40iterations 1.105415 21.89926 at 50iterations 0.6380213 12.83349 at 60iterations 0.3680207 6.840031 at 70iterations 0.2120555 3.756355 at 80iterations 0.1220217 2.288837 at 90iterations 7.0451386E-02 1.257909 at 100iterations 4.0533941E-02 0.7516794 at 110iterations 2.3370301E-02 0.4267216 at 120iterations 1.3470454E-02 0.2290039 at 130iterations 7.7531911E-03 0.1343079 at 140iterations 4.4673756E-03 8.5190833E-02 at 150iterations 2.5854458E-03 4.7098160E-02 at 160iterations 1.4945721E-03 2.8900146E-02 at 170iterations 8.6448470E-04 1.6671419E-02 at 180iterations finished qdiffx linear iterations at : 19:49:48 total time elapsed so far: 15.54000 # loops : 180 mean,max change (kT/e) : 8.6448470E-04 1.6671419E-02 energy calculations done at 15.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.72000 DelPhi exited at 19:49:49 15.719u 0.317s 0:16.31 98.2% 0+0k 0+0io 0pf+0w