Mon Oct 10 09:23:20 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 Mon Oct 10 2011 at 09:23:20 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2752 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: 0.5709245 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): -15.13400 35.45600 ymin,ymax (A): -67.56300 -9.298000 zmin,zma (A): 4.9000025E-02 62.40400 x,y,z range (A): 50.59000 58.26500 62.35500 scale (grids/A): 0.5709245 object centre (A): 10.16100 -38.43050 31.22650 number of atom coordinates read : 2752 total number of charged atoms : 2603 net assigned charge : 5.000009 assigned positive charge : 403.8080 centred at (gu) : 89.13315 89.20247 87.44479 assigned negative charge : -398.8084 centred at (gu) : 89.14388 89.05767 87.41721 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6165 nv = 96 ne = 84 npr = 51853 no. pairs analyzed = 51853 no. exposed pairs = 4279 no. arc points = 31185 no. surface atoms = 1411 nbur = 1341 mkacc time = 0.1400000 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 = 1.512000 m= 296 mr = 2615 m= 3 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.3200000 number of dielectric boundary points 3826 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3188 ## 362 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7799 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.3661738E-10 6.7208256E-10 midg,1,midg; midg,igrid,midg -1.5953692E-09 2.3710736E-09 1,midg,midg; igrid,midg,midg 1.1877324E-09 5.4301130E-10 gauss-seidel spectral radius is 0.9841747 estimated iterations to convergence 65 setup time was (sec) 0.6600000 now iterating at: 09:23:21 rms-change max change #iterations 8.3711885E-02 13.76175 at 10iterations 6.1362823E-03 0.9865303 at 20iterations 4.8266290E-04 8.2025528E-02 at 30iterations 4.1753727E-05 6.4687729E-03 at 40iterations 6.1092051E-06 7.7056885E-04 at 50iterations finished qdiffx linear iterations at : 09:23:26 total time elapsed so far: 5.120000 # loops : 50 mean,max change (kT/e) : 6.1092051E-06 7.7056885E-04 energy calculations done at 5.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.290000 DelPhi exited at 09:23:26 5.293u 0.444s 0:06.01 95.3% 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 Mon Oct 10 2011 at 09:23:26 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2752 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: 1.712774 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): -15.13400 35.45600 ymin,ymax (A): -67.56300 -9.298000 zmin,zma (A): 4.9000025E-02 62.40400 x,y,z range (A): 50.59000 58.26500 62.35500 scale (grids/A): 1.712774 object centre (A): 10.16100 -38.43050 31.22650 number of atom coordinates read : 2752 total number of charged atoms : 2603 net assigned charge : 5.000009 assigned positive charge : 403.8080 centred at (gu) : 87.39893 87.60710 82.33397 assigned negative charge : -398.8084 centred at (gu) : 87.43148 87.17270 82.25149 start vw surface at 0.1300000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 65707 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31185 grid for indexing accessible points = 1.400000 m= 20663 mr = 39311 m= 2766 mr = 12955 m= 117 mr = 1326 m= 0 mr = 9 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 35652 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 310 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 20163 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) : 0.5709245 object centre at (A) : 10.16100 -38.43050 31.22650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6009809E-02 9.8955985E-03 midg,1,midg; midg,igrid,midg 5.7255109E-03 2.2386396E-02 1,midg,midg; igrid,midg,midg 5.2200741E-04 1.4791659E-03 gauss-seidel spectral radius is 0.9983644 estimated iterations to convergence 196 setup time was (sec) 0.9800000 now iterating at: 09:23:28 rms-change max change #iterations 3.472995 183.7247 at 10iterations 1.500818 63.68901 at 20iterations 0.6498544 25.47319 at 30iterations 0.2821438 10.43635 at 40iterations 0.1231876 4.628550 at 50iterations 5.3174119E-02 2.050629 at 60iterations 2.3137927E-02 0.8308105 at 70iterations 1.0058992E-02 0.3662868 at 80iterations 4.3733674E-03 0.1636777 at 90iterations 1.9001431E-03 6.8698883E-02 at 100iterations 8.3058403E-04 3.3035278E-02 at 110iterations 3.6047676E-04 1.3467073E-02 at 120iterations finished qdiffx linear iterations at : 09:23:39 total time elapsed so far: 12.56000 # loops : 120 mean,max change (kT/e) : 3.6047676E-04 1.3467073E-02 energy calculations done at 12.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.72000 DelPhi exited at 09:23:40 12.725u 0.529s 0:13.63 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 Mon Oct 10 2011 at 09:23:40 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2752 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: 2.569160 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): -15.13400 35.45600 ymin,ymax (A): -67.56300 -9.298000 zmin,zma (A): 4.9000025E-02 62.40400 x,y,z range (A): 50.59000 58.26500 62.35500 scale (grids/A): 2.569160 object centre (A): 10.16100 -38.43050 31.22650 number of atom coordinates read : 2752 total number of charged atoms : 2603 net assigned charge : 5.000009 assigned positive charge : 403.8080 centred at (gu) : 86.09825 86.41049 78.50087 assigned negative charge : -398.8084 centred at (gu) : 86.14713 85.75887 78.37717 start vw surface at 0.1200000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 152043 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31185 grid for indexing accessible points = 1.400000 m= 67816 mr = 97727 m= 22029 mr = 49996 m= 4454 mr = 15714 m= 411 mr = 2743 m= 9 mr = 188 m= 0 mr = 2 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.460000 number of dielectric boundary points 80392 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 20814 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) : 1.712774 object centre at (A) : 10.16100 -38.43050 31.22650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9379725E-02 5.6702904E-02 midg,1,midg; midg,igrid,midg 0.2828420 0.3024201 1,midg,midg; igrid,midg,midg 1.9463646E-03 4.0141143E-02 gauss-seidel spectral radius is 0.9992125 estimated iterations to convergence 281 setup time was (sec) 1.870000 now iterating at: 09:23:42 rms-change max change #iterations 9.062086 306.4584 at 10iterations 5.333850 156.3212 at 20iterations 3.102614 84.21919 at 30iterations 1.790642 43.92895 at 40iterations 1.028026 24.96097 at 50iterations 0.5869438 15.52007 at 60iterations 0.3349186 6.770861 at 70iterations 0.1907893 4.151157 at 80iterations 0.1085542 2.310635 at 90iterations 6.1325978E-02 1.366631 at 100iterations 3.4824200E-02 0.7400970 at 110iterations 1.9698838E-02 0.4265022 at 120iterations 1.1127281E-02 0.2363434 at 130iterations 6.2859273E-03 0.1258283 at 140iterations 3.5562010E-03 7.0463181E-02 at 150iterations 2.0040739E-03 3.8996458E-02 at 160iterations 1.1323621E-03 2.3036957E-02 at 170iterations 6.3785352E-04 1.2308121E-02 at 180iterations finished qdiffx linear iterations at : 09:24:02 total time elapsed so far: 21.79000 # loops : 180 mean,max change (kT/e) : 6.3785352E-04 1.2308121E-02 energy calculations done at 21.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.96000 DelPhi exited at 09:24:03 21.967u 0.535s 0:22.78 98.7% 0+0k 0+0io 0pf+0w