Sat Oct 15 12:56:48 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 15 2011 at 12:56:48 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 = 2286 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7125273 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): -19.32700 29.74400 ymin,ymax (A): -20.91400 29.04900 zmin,zma (A): 2.585000 46.15100 x,y,z range (A): 49.07100 49.96300 43.56600 scale (grids/A): 0.7125273 object centre (A): 5.208500 4.067500 24.36800 number of atom coordinates read : 2286 total number of charged atoms : 2146 net assigned charge : 5.500010 assigned positive charge : 346.0692 centred at (gu) : 90.40546 90.53969 90.42039 assigned negative charge : -340.5697 centred at (gu) : 90.45906 90.58908 90.50683 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8065 nv = 96 ne = 84 npr = 45476 no. pairs analyzed = 45476 no. exposed pairs = 2815 no. arc points = 20046 no. surface atoms = 950 nbur = 1336 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 546 mr = 4556 m= 6 mr = 102 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1917 ## 179 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8750 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.6529270E-08 -3.1391074E-11 midg,1,midg; midg,igrid,midg 7.4512428E-08 2.5136316E-08 1,midg,midg; igrid,midg,midg 7.8754788E-08 2.1780906E-08 gauss-seidel spectral radius is 0.9897584 estimated iterations to convergence 80 setup time was (sec) 0.3900000 now iterating at: 12:56:48 rms-change max change #iterations 0.2127860 26.31933 at 10iterations 2.7123956E-02 3.353745 at 20iterations 3.7370161E-03 0.5474930 at 30iterations 7.4395735E-04 0.1150103 at 40iterations 2.3669614E-04 3.7685394E-02 at 50iterations finished qdiffx linear iterations at : 12:56:52 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 2.3669614E-04 3.7685394E-02 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 12:56:53 3.462u 0.217s 0:05.42 67.7% 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 Sat Oct 15 2011 at 12:56:53 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 = 2286 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.137582 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): -19.32700 29.74400 ymin,ymax (A): -20.91400 29.04900 zmin,zma (A): 2.585000 46.15100 x,y,z range (A): 49.07100 49.96300 43.56600 scale (grids/A): 2.137582 object centre (A): 5.208500 4.067500 24.36800 number of atom coordinates read : 2286 total number of charged atoms : 2146 net assigned charge : 5.500010 assigned positive charge : 346.0692 centred at (gu) : 91.21586 91.61869 91.26074 assigned negative charge : -340.5697 centred at (gu) : 91.37682 91.76707 91.52041 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 85409 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20046 grid for indexing accessible points = 1.400000 m= 34150 mr = 59951 m= 6830 mr = 25960 m= 660 mr = 4580 m= 19 mr = 332 m= 0 mr = 2 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 36243 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 17079 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) : 0.7125273 object centre at (A) : 5.208500 4.067500 24.36800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6697799E-02 7.5154044E-03 midg,1,midg; midg,igrid,midg -5.6214682E-03 -6.6746056E-02 1,midg,midg; igrid,midg,midg -6.6404706E-03 8.4406644E-04 gauss-seidel spectral radius is 0.9988764 estimated iterations to convergence 236 setup time was (sec) 0.6700000 now iterating at: 12:56:54 rms-change max change #iterations 4.946127 241.7747 at 10iterations 2.468119 75.36264 at 20iterations 1.239848 39.83056 at 30iterations 0.6221464 19.99215 at 40iterations 0.3141971 8.530228 at 50iterations 0.1579691 5.397490 at 60iterations 7.9476140E-02 2.150236 at 70iterations 4.0172063E-02 1.323032 at 80iterations 2.0268569E-02 0.6100059 at 90iterations 1.0310116E-02 0.2855721 at 100iterations 5.2966801E-03 0.1558990 at 110iterations 2.7754274E-03 9.1232300E-02 at 120iterations finished qdiffx linear iterations at : 12:57:02 total time elapsed so far: 8.350000 # loops : 120 mean,max change (kT/e) : 2.7754274E-03 9.1232300E-02 energy calculations done at 8.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.490000 DelPhi exited at 12:57:02 8.494u 0.221s 0:09.15 95.1% 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 Sat Oct 15 2011 at 12:57:02 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 = 2286 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.206373 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): -19.32700 29.74400 ymin,ymax (A): -20.91400 29.04900 zmin,zma (A): 2.585000 46.15100 x,y,z range (A): 49.07100 49.96300 43.56600 scale (grids/A): 3.206373 object centre (A): 5.208500 4.067500 24.36800 number of atom coordinates read : 2286 total number of charged atoms : 2146 net assigned charge : 5.500010 assigned positive charge : 346.0692 centred at (gu) : 91.82381 92.42790 91.89104 assigned negative charge : -340.5697 centred at (gu) : 92.06514 92.65057 92.28062 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 196577 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20046 grid for indexing accessible points = 1.400000 m= 106305 mr = 144157 m= 43696 mr = 88466 m= 12996 mr = 35741 m= 2682 mr = 10224 m= 318 mr = 1986 m= 22 mr = 197 m= 0 mr = 11 time to grow re-entrant surface = 0.6999999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.340000 number of dielectric boundary points 81814 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 17167 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) : 2.137582 object centre at (A) : 5.208500 4.067500 24.36800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5504220 -5.8928773E-02 midg,1,midg; midg,igrid,midg -0.4917278 -0.9330504 1,midg,midg; igrid,midg,midg -0.2343208 -0.1612917 gauss-seidel spectral radius is 0.9993114 estimated iterations to convergence 301 setup time was (sec) 1.600000 now iterating at: 12:57:04 rms-change max change #iterations 10.98487 404.0645 at 10iterations 6.554126 153.1086 at 20iterations 3.891169 74.39517 at 30iterations 2.312207 43.95024 at 40iterations 1.365744 24.32118 at 50iterations 0.8088700 13.56149 at 60iterations 0.4772935 8.164868 at 70iterations 0.2810144 5.057034 at 80iterations 0.1655926 2.748294 at 90iterations 9.7689077E-02 1.731567 at 100iterations 5.7608716E-02 0.9255981 at 110iterations 3.4108531E-02 0.5701599 at 120iterations 2.0323081E-02 0.3520966 at 130iterations 1.2288238E-02 0.2152974 at 140iterations 7.6140636E-03 0.1402054 at 150iterations 4.9250447E-03 0.1024380 at 160iterations 3.3748464E-03 7.1044922E-02 at 170iterations 2.4677361E-03 5.1586151E-02 at 180iterations finished qdiffx linear iterations at : 12:57:17 total time elapsed so far: 14.22000 # loops : 180 mean,max change (kT/e) : 2.4677361E-03 5.1586151E-02 energy calculations done at 14.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.36000 DelPhi exited at 12:57:17 14.358u 0.272s 0:14.92 97.9% 0+0k 0+0io 0pf+0w