Sun Oct 9 06:40:06 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 06:40:06 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: 391 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2665 !!! WARNING: GLM 35 has a net charge of -0.0940 !!! WARNING: ASP 371 has a net charge of -0.0260 !!! WARNING: NDP 372 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5215964 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): -27.99500 34.79900 ymin,ymax (A): -0.2840000 57.76900 zmin,zma (A): -26.90700 41.34500 x,y,z range (A): 62.79400 58.05300 68.25200 scale (grids/A): 0.5215964 object centre (A): 3.401999 28.74250 7.218999 number of atom coordinates read : 2665 total number of charged atoms : 2468 net assigned charge : -2.119983 assigned positive charge : 392.8939 centred at (gu) : 90.76711 89.89188 87.88188 assigned negative charge : -395.0145 centred at (gu) : 90.91295 89.86617 87.92403 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 4763 nv = 96 ne = 84 npr = 52492 no. pairs analyzed = 52492 no. exposed pairs = 3740 no. arc points = 27332 no. surface atoms = 1246 nbur = 1419 mkacc time = 0.1500000 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 = 1.624000 m= 174 mr = 2187 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3400000 number of dielectric boundary points 2749 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2645 ## 388 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 6231 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.5113937E-11 -8.3353477E-11 midg,1,midg; midg,igrid,midg -1.0867091E-10 1.0105335E-11 1,midg,midg; igrid,midg,midg 2.2537455E-10 -4.6867799E-10 gauss-seidel spectral radius is 0.9810565 estimated iterations to convergence 60 setup time was (sec) 0.6000000 now iterating at: 06:40:07 rms-change max change #iterations 5.5027328E-02 11.40042 at 10iterations 3.1581235E-03 0.5553207 at 20iterations 1.8132098E-04 3.5022736E-02 at 30iterations 1.0737172E-05 2.0828247E-03 at 40iterations 6.4300110E-07 1.1444092E-04 at 50iterations finished qdiffx linear iterations at : 06:40:10 total time elapsed so far: 3.920000 # loops : 50 mean,max change (kT/e) : 6.4300110E-07 1.1444092E-04 energy calculations done at 3.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.100000 DelPhi exited at 06:40:11 4.101u 0.275s 0:04.66 93.7% 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 Sun Oct 9 2011 at 06:40:11 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: 391 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2665 !!! WARNING: GLM 35 has a net charge of -0.0940 !!! WARNING: ASP 371 has a net charge of -0.0260 !!! WARNING: NDP 372 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.564789 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): -27.99500 34.79900 ymin,ymax (A): -0.2840000 57.76900 zmin,zma (A): -26.90700 41.34500 x,y,z range (A): 62.79400 58.05300 68.25200 scale (grids/A): 1.564789 object centre (A): 3.401999 28.74250 7.218999 number of atom coordinates read : 2665 total number of charged atoms : 2468 net assigned charge : -2.119983 assigned positive charge : 392.8939 centred at (gu) : 92.30099 89.67531 83.64510 assigned negative charge : -395.0145 centred at (gu) : 92.73852 89.59833 83.77184 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 53113 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27332 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 14080 mr = 33528 m= 1150 mr = 8744 m= 29 mr = 444 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1129 time to turn everything in is 0.5100000 number of dielectric boundary points 25656 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 341 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 18704 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) : 0.5215964 object centre at (A) : 3.401999 28.74250 7.218999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7506387E-02 -5.8680866E-03 midg,1,midg; midg,igrid,midg 1.6717650E-03 2.3430111E-03 1,midg,midg; igrid,midg,midg -1.3255875E-03 -7.7158217E-03 gauss-seidel spectral radius is 0.9979885 estimated iterations to convergence 177 setup time was (sec) 0.8100000 now iterating at: 06:40:12 rms-change max change #iterations 2.830018 208.2379 at 10iterations 1.122233 85.87253 at 20iterations 0.4425820 21.13795 at 30iterations 0.1753147 7.357880 at 40iterations 6.9644414E-02 4.172653 at 50iterations 2.7777620E-02 1.292515 at 60iterations 1.1011465E-02 0.4888000 at 70iterations 4.3949522E-03 0.1996307 at 80iterations 1.7359585E-03 6.6482544E-02 at 90iterations 6.9145468E-04 3.0975342E-02 at 100iterations 2.7580946E-04 1.2221336E-02 at 110iterations 1.0948278E-04 4.4441223E-03 at 120iterations finished qdiffx linear iterations at : 06:40:20 total time elapsed so far: 8.980000 # loops : 120 mean,max change (kT/e) : 1.0948278E-04 4.4441223E-03 energy calculations done at 8.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.150000 DelPhi exited at 06:40:21 9.153u 0.286s 0:09.71 97.1% 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 06:40:21 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: 391 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2665 !!! WARNING: GLM 35 has a net charge of -0.0940 !!! WARNING: ASP 371 has a net charge of -0.0260 !!! WARNING: NDP 372 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.347184 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): -27.99500 34.79900 ymin,ymax (A): -0.2840000 57.76900 zmin,zma (A): -26.90700 41.34500 x,y,z range (A): 62.79400 58.05300 68.25200 scale (grids/A): 2.347184 object centre (A): 3.401999 28.74250 7.218999 number of atom coordinates read : 2665 total number of charged atoms : 2468 net assigned charge : -2.119983 assigned positive charge : 392.8939 centred at (gu) : 93.45133 89.51275 80.46752 assigned negative charge : -395.0145 centred at (gu) : 94.10771 89.39749 80.65771 start vw surface at 0.1600000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 123396 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27332 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 50812 mr = 82603 m= 11989 mr = 38242 m= 1614 mr = 8160 m= 89 mr = 934 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 3737 time to turn everything in is 1.170000 number of dielectric boundary points 57935 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 40 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 19710 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) : 1.564789 object centre at (A) : 3.401999 28.74250 7.218999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5223767 -2.8509738E-02 midg,1,midg; midg,igrid,midg 7.2732806E-02 2.2317603E-02 1,midg,midg; igrid,midg,midg 1.3105099E-02 -9.6760161E-02 gauss-seidel spectral radius is 0.9990694 estimated iterations to convergence 259 setup time was (sec) 1.480000 now iterating at: 06:40:23 rms-change max change #iterations 7.638372 283.5884 at 10iterations 4.201950 122.1000 at 20iterations 2.305021 64.36768 at 30iterations 1.259226 33.42577 at 40iterations 0.6808166 18.88074 at 50iterations 0.3693476 9.622209 at 60iterations 0.1990157 4.779206 at 70iterations 0.1073310 2.711807 at 80iterations 5.7735980E-02 1.313478 at 90iterations 3.1054232E-02 0.7226238 at 100iterations 1.6674889E-02 0.3764279 at 110iterations 8.9452565E-03 0.2061577 at 120iterations 4.8039663E-03 0.1195450 at 130iterations 2.5744431E-03 7.2020531E-02 at 140iterations 1.3825032E-03 2.9747009E-02 at 150iterations 7.4030744E-04 1.8144608E-02 at 160iterations 3.9586186E-04 8.6898804E-03 at 170iterations 2.1276821E-04 6.0100555E-03 at 180iterations finished qdiffx linear iterations at : 06:40:36 total time elapsed so far: 14.65000 # loops : 180 mean,max change (kT/e) : 2.1276821E-04 6.0100555E-03 energy calculations done at 14.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.83000 DelPhi exited at 06:40:36 14.827u 0.328s 0:15.45 97.9% 0+0k 0+0io 0pf+0w