Sun Oct 9 13:06:51 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 13:06:51 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2424 !!! WARNING: GLM 182 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6793116 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): -15.62000 34.23700 ymin,ymax (A): -13.76000 38.64600 zmin,zma (A): 34.76200 76.95500 x,y,z range (A): 49.85700 52.40600 42.19300 scale (grids/A): 0.6793116 object centre (A): 9.308501 12.44300 55.85850 number of atom coordinates read : 2424 total number of charged atoms : 2278 net assigned charge : 5.406020 assigned positive charge : 373.8119 centred at (gu) : 90.47347 90.85775 89.10843 assigned negative charge : -368.4065 centred at (gu) : 90.50062 90.98340 88.98814 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7265 nv = 96 ne = 84 npr = 49838 no. pairs analyzed = 49838 no. exposed pairs = 2846 no. arc points = 19941 no. surface atoms = 967 nbur = 1457 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 407 mr = 4069 m= 0 mr = 60 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.1900000 number of dielectric boundary points 3543 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1939 ## 175 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8572 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6305082E-08 4.9850403E-08 midg,1,midg; midg,igrid,midg 5.1516629E-08 -1.8169944E-08 1,midg,midg; igrid,midg,midg 2.8990145E-08 1.6826636E-08 gauss-seidel spectral radius is 0.9887415 estimated iterations to convergence 77 setup time was (sec) 0.4000000 now iterating at: 13:06:52 rms-change max change #iterations 0.1841832 27.33563 at 10iterations 2.1319441E-02 2.785044 at 20iterations 2.6002831E-03 0.3702413 at 30iterations 3.8792001E-04 5.6083679E-02 at 40iterations 8.3539860E-05 1.0086060E-02 at 50iterations finished qdiffx linear iterations at : 13:06:55 total time elapsed so far: 3.560000 # loops : 50 mean,max change (kT/e) : 8.3539860E-05 1.0086060E-02 energy calculations done at 3.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.700000 DelPhi exited at 13:06:56 3.703u 0.185s 0:04.40 88.1% 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 13:06:56 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2424 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 2.037935 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): -15.62000 34.23700 ymin,ymax (A): -13.76000 38.64600 zmin,zma (A): 34.76200 76.95500 x,y,z range (A): 49.85700 52.40600 42.19300 scale (grids/A): 2.037935 object centre (A): 9.308501 12.44300 55.85850 number of atom coordinates read : 2424 total number of charged atoms : 2278 net assigned charge : 5.406020 assigned positive charge : 373.8119 centred at (gu) : 91.41975 92.57276 87.32472 assigned negative charge : -368.4065 centred at (gu) : 91.50171 92.94978 86.96405 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 77895 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19941 grid for indexing accessible points = 1.400000 m= 28742 mr = 54654 m= 4908 mr = 21375 m= 403 mr = 3113 m= 3 mr = 201 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 83 time to turn everything in is 0.4100000 number of dielectric boundary points 32608 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 18028 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) : 0.6793116 object centre at (A) : 9.308501 12.44300 55.85850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.3228254E-04 5.5573530E-02 midg,1,midg; midg,igrid,midg 3.2944266E-02 -1.4959950E-02 1,midg,midg; igrid,midg,midg 1.1020511E-02 4.5413695E-02 gauss-seidel spectral radius is 0.9987763 estimated iterations to convergence 226 setup time was (sec) 0.6400000 now iterating at: 13:06:57 rms-change max change #iterations 4.744619 237.1604 at 10iterations 2.308093 104.7885 at 20iterations 1.130283 38.63997 at 30iterations 0.5531664 16.14167 at 40iterations 0.2691897 8.657364 at 50iterations 0.1309964 4.128670 at 60iterations 6.4113572E-02 1.995388 at 70iterations 3.1223319E-02 0.9435916 at 80iterations 1.5376430E-02 0.5081164 at 90iterations 7.5287013E-03 0.2145405 at 100iterations 3.7059111E-03 0.1107231 at 110iterations 1.8393381E-03 5.5942535E-02 at 120iterations finished qdiffx linear iterations at : 13:07:04 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 1.8393381E-03 5.5942535E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 13:07:05 7.973u 0.229s 0:08.77 93.3% 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 Sun Oct 9 2011 at 13:07:05 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2424 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 3.056902 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): -15.62000 34.23700 ymin,ymax (A): -13.76000 38.64600 zmin,zma (A): 34.76200 76.95500 x,y,z range (A): 49.85700 52.40600 42.19300 scale (grids/A): 3.056902 object centre (A): 9.308501 12.44300 55.85850 number of atom coordinates read : 2424 total number of charged atoms : 2278 net assigned charge : 5.406020 assigned positive charge : 373.8119 centred at (gu) : 92.12969 93.85884 85.98701 assigned negative charge : -368.4065 centred at (gu) : 92.25242 94.42472 85.44608 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 180047 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19941 grid for indexing accessible points = 1.400000 m= 92554 mr = 132243 m= 34430 mr = 76279 m= 8990 mr = 27813 m= 1668 mr = 6766 m= 187 mr = 1193 m= 2 mr = 112 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 246 time to turn everything in is 1.030000 number of dielectric boundary points 73472 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 18224 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) : 2.037935 object centre at (A) : 9.308501 12.44300 55.85850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1077544 0.5142651 midg,1,midg; midg,igrid,midg 0.8327746 -5.1477835E-02 1,midg,midg; igrid,midg,midg -8.2653917E-02 0.5812083 gauss-seidel spectral radius is 0.9992856 estimated iterations to convergence 295 setup time was (sec) 1.270000 now iterating at: 13:07:06 rms-change max change #iterations 10.74963 342.5480 at 10iterations 6.323689 134.9062 at 20iterations 3.712787 79.69101 at 30iterations 2.173632 41.19918 at 40iterations 1.274956 24.30606 at 50iterations 0.7439126 14.12958 at 60iterations 0.4335642 7.912819 at 70iterations 0.2528502 4.368162 at 80iterations 0.1474729 2.526577 at 90iterations 8.5875429E-02 1.466401 at 100iterations 5.0156228E-02 1.002607 at 110iterations 2.9273393E-02 0.5288467 at 120iterations 1.7166346E-02 0.2978745 at 130iterations 1.0078855E-02 0.1930275 at 140iterations 6.0062790E-03 0.1060944 at 150iterations 3.6309073E-03 6.9793701E-02 at 160iterations 2.2535566E-03 4.9171448E-02 at 170iterations 1.4486877E-03 3.1440735E-02 at 180iterations finished qdiffx linear iterations at : 13:07:18 total time elapsed so far: 12.74000 # loops : 180 mean,max change (kT/e) : 1.4486877E-03 3.1440735E-02 energy calculations done at 12.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.89000 DelPhi exited at 13:07:18 12.893u 0.219s 0:13.43 97.5% 0+0k 0+0io 0pf+0w