Sat Oct 15 11:26:58 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 Sat Oct 15 2011 at 11:26:58 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2580 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! 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 556 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6266613 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): -31.71200 17.51600 ymin,ymax (A): -23.52600 22.86800 zmin,zma (A): -11.62800 45.18100 x,y,z range (A): 49.22800 46.39400 56.80900 scale (grids/A): 0.6266613 object centre (A): -7.098000 -0.3289995 16.77650 number of atom coordinates read : 2580 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 391.8441 centred at (gu) : 88.42225 89.21886 89.40990 assigned negative charge : -387.9385 centred at (gu) : 88.31730 89.25922 89.29942 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6525 nv = 96 ne = 84 npr = 53685 no. pairs analyzed = 53685 no. exposed pairs = 2954 no. arc points = 20892 no. surface atoms = 1000 nbur = 1580 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 336 mr = 3664 m= 1 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 117 time to turn everything in is 0.2000000 number of dielectric boundary points 3150 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2092 ## 184 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8097 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.6672875E-09 1.1226930E-08 midg,1,midg; midg,igrid,midg 8.5813774E-09 6.8107536E-10 1,midg,midg; igrid,midg,midg -6.4993237E-09 8.7646850E-09 gauss-seidel spectral radius is 0.9868031 estimated iterations to convergence 71 setup time was (sec) 0.4400000 now iterating at: 11:26:58 rms-change max change #iterations 0.1345010 21.29168 at 10iterations 1.2746020E-02 1.642128 at 20iterations 1.2128268E-03 0.1663904 at 30iterations 1.1338890E-04 1.9210815E-02 at 40iterations 1.0811210E-05 1.6260147E-03 at 50iterations finished qdiffx linear iterations at : 11:27:02 total time elapsed so far: 3.840000 # loops : 50 mean,max change (kT/e) : 1.0811210E-05 1.6260147E-03 energy calculations done at 3.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.990000 DelPhi exited at 11:27:02 3.989u 0.287s 0:04.65 91.6% 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 Sat Oct 15 2011 at 11:27:02 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2580 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! 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 556 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.879984 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): -31.71200 17.51600 ymin,ymax (A): -23.52600 22.86800 zmin,zma (A): -11.62800 45.18100 x,y,z range (A): 49.22800 46.39400 56.80900 scale (grids/A): 1.879984 object centre (A): -7.098000 -0.3289995 16.77650 number of atom coordinates read : 2580 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 391.8441 centred at (gu) : 85.26597 87.65623 88.22957 assigned negative charge : -387.9385 centred at (gu) : 84.95191 87.77750 87.89796 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 71478 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20892 grid for indexing accessible points = 1.400000 m= 25174 mr = 50350 m= 3675 mr = 18942 m= 199 mr = 2287 m= 2 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 5902 time to turn everything in is 0.3500000 number of dielectric boundary points 28869 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 124 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 19213 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) : 0.6266613 object centre at (A) : -7.098000 -0.3289995 16.77650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7227722E-02 2.6723281E-02 midg,1,midg; midg,igrid,midg 1.1686506E-02 1.3142596E-03 1,midg,midg; igrid,midg,midg -8.3330767E-03 3.2405369E-02 gauss-seidel spectral radius is 0.9985909 estimated iterations to convergence 211 setup time was (sec) 0.5800000 now iterating at: 11:27:03 rms-change max change #iterations 4.119917 170.6499 at 10iterations 1.907155 62.52947 at 20iterations 0.8841866 29.46586 at 30iterations 0.4084567 14.00503 at 40iterations 0.1894012 5.949211 at 50iterations 8.7542109E-02 2.924862 at 60iterations 4.0635165E-02 1.294622 at 70iterations 1.8779499E-02 0.6288929 at 80iterations 8.6982595E-03 0.2677307 at 90iterations 4.0310854E-03 0.1413383 at 100iterations 1.8639324E-03 5.4981232E-02 at 110iterations 8.6361979E-04 2.7963638E-02 at 120iterations finished qdiffx linear iterations at : 11:27:12 total time elapsed so far: 9.170000 # loops : 120 mean,max change (kT/e) : 8.6361979E-04 2.7963638E-02 energy calculations done at 9.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.310000 DelPhi exited at 11:27:12 9.313u 0.309s 0:10.12 94.9% 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 15 2011 at 11:27:13 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2580 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! 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 556 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.819976 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): -31.71200 17.51600 ymin,ymax (A): -23.52600 22.86800 zmin,zma (A): -11.62800 45.18100 x,y,z range (A): 49.22800 46.39400 56.80900 scale (grids/A): 2.819976 object centre (A): -7.098000 -0.3289995 16.77650 number of atom coordinates read : 2580 total number of charged atoms : 2450 net assigned charge : 3.906008 assigned positive charge : 391.8441 centred at (gu) : 82.89890 86.48409 87.34425 assigned negative charge : -387.9385 centred at (gu) : 82.42779 86.66631 86.84694 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 165520 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20892 grid for indexing accessible points = 1.400000 m= 83378 mr = 121627 m= 28637 mr = 69241 m= 6508 mr = 23391 m= 867 mr = 4933 m= 64 mr = 569 m= 5 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 19908 time to turn everything in is 1.000000 number of dielectric boundary points 65183 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 19596 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) : 1.879984 object centre at (A) : -7.098000 -0.3289995 16.77650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.7151065E-02 0.3142872 midg,1,midg; midg,igrid,midg 0.1476919 -3.0495231E-03 1,midg,midg; igrid,midg,midg -7.9030156E-02 0.4254480 gauss-seidel spectral radius is 0.9992397 estimated iterations to convergence 286 setup time was (sec) 1.320000 now iterating at: 11:27:14 rms-change max change #iterations 9.592823 290.8731 at 10iterations 5.489287 113.7760 at 20iterations 3.123231 60.81678 at 30iterations 1.779280 33.39776 at 40iterations 1.013805 18.28580 at 50iterations 0.5772351 10.17431 at 60iterations 0.3285720 6.474911 at 70iterations 0.1871622 3.413261 at 80iterations 0.1062648 1.980772 at 90iterations 6.0646020E-02 1.217127 at 100iterations 3.4511581E-02 0.6136780 at 110iterations 1.9626839E-02 0.3948364 at 120iterations 1.1184787E-02 0.1977768 at 130iterations 6.3610561E-03 0.1296921 at 140iterations 3.6154338E-03 7.2286606E-02 at 150iterations 2.0581586E-03 3.7388533E-02 at 160iterations 1.1733243E-03 2.0172119E-02 at 170iterations 6.6804857E-04 1.4617920E-02 at 180iterations finished qdiffx linear iterations at : 11:27:29 total time elapsed so far: 15.51000 # loops : 180 mean,max change (kT/e) : 6.6804857E-04 1.4617920E-02 energy calculations done at 15.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.65000 DelPhi exited at 11:27:29 15.653u 0.415s 0:16.55 97.0% 0+0k 0+0io 0pf+0w