Wed Feb 15 08:55:30 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:55:30 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: 223 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2781 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5807315 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): -23.14500 19.83500 ymin,ymax (A): -41.04400 20.25800 zmin,zma (A): -22.57400 31.75800 x,y,z range (A): 42.98000 61.30200 54.33200 scale (grids/A): 0.5807315 object centre (A): -1.655001 -10.39300 4.592001 number of atom coordinates read : 2781 total number of charged atoms : 2651 net assigned charge : -0.4999969 assigned positive charge : 379.1896 centred at (gu) : 91.98788 90.39842 89.99960 assigned negative charge : -379.6906 centred at (gu) : 91.97378 90.25903 89.99861 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6288 nv = 96 ne = 84 npr = 58447 no. pairs analyzed = 58447 no. exposed pairs = 3594 no. arc points = 25657 no. surface atoms = 1223 nbur = 1558 mkacc time = 0.1300000 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 = 1.456000 m= 312 mr = 3116 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3463 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2498 ## 204 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7900 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4669796E-10 -1.0868275E-10 midg,1,midg; midg,igrid,midg -2.5896660E-09 2.7522895E-09 1,midg,midg; igrid,midg,midg -2.5129443E-10 2.3411420E-10 gauss-seidel spectral radius is 0.9846911 estimated iterations to convergence 66 setup time was (sec) 0.5600000 now iterating at: 08:55:31 rms-change max change #iterations 9.1387287E-02 15.34224 at 10iterations 8.2109803E-03 1.413790 at 20iterations 1.9261411E-03 0.3808136 at 30iterations 7.9355988E-04 0.1628036 at 40iterations 3.4099678E-04 6.9984436E-02 at 50iterations finished qdiffx linear iterations at : 08:55:33 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 3.4099678E-04 6.9984436E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 08:55:34 3.398u 0.155s 0:03.87 91.4% 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 Wed Feb 15 2012 at 08:55:34 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: 223 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2781 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.742194 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): -23.14500 19.83500 ymin,ymax (A): -41.04400 20.25800 zmin,zma (A): -22.57400 31.75800 x,y,z range (A): 42.98000 61.30200 54.33200 scale (grids/A): 1.742194 object centre (A): -1.655001 -10.39300 4.592001 number of atom coordinates read : 2781 total number of charged atoms : 2651 net assigned charge : -0.4999969 assigned positive charge : 379.1896 centred at (gu) : 95.96297 91.19487 89.99844 assigned negative charge : -379.6906 centred at (gu) : 95.92087 90.77683 89.99566 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 68197 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25657 grid for indexing accessible points = 1.400000 m= 23189 mr = 44741 m= 3504 mr = 16106 m= 134 mr = 2106 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 32053 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 20616 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) : 0.5807315 object centre at (A) : -1.655001 -10.39300 4.592001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5378414E-03 -6.7083533E-03 midg,1,midg; midg,igrid,midg -6.1263405E-03 1.1574070E-02 1,midg,midg; igrid,midg,midg 8.4932096E-04 4.1373883E-04 gauss-seidel spectral radius is 0.9984002 estimated iterations to convergence 198 setup time was (sec) 0.8700000 now iterating at: 08:55:35 rms-change max change #iterations 3.476048 142.6642 at 10iterations 1.518581 59.77213 at 20iterations 0.6666360 24.36851 at 30iterations 0.2942197 9.881344 at 40iterations 0.1295307 5.057985 at 50iterations 5.7050552E-02 2.161335 at 60iterations 2.5608227E-02 0.9108562 at 70iterations 1.1837468E-02 0.4314346 at 80iterations 5.8863801E-03 0.2468567 at 90iterations 3.3139854E-03 0.1490650 at 100iterations 2.1207128E-03 8.5113525E-02 at 110iterations 1.4884731E-03 6.2059402E-02 at 120iterations finished qdiffx linear iterations at : 08:55:43 total time elapsed so far: 8.980000 # loops : 120 mean,max change (kT/e) : 1.4884731E-03 6.2059402E-02 energy calculations done at 8.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.180000 DelPhi exited at 08:55:44 9.183u 0.243s 0:10.32 91.2% 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 Wed Feb 15 2012 at 08:55:44 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: 223 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2781 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.613292 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): -23.14500 19.83500 ymin,ymax (A): -41.04400 20.25800 zmin,zma (A): -22.57400 31.75800 x,y,z range (A): 42.98000 61.30200 54.33200 scale (grids/A): 2.613292 object centre (A): -1.655001 -10.39300 4.592001 number of atom coordinates read : 2781 total number of charged atoms : 2651 net assigned charge : -0.4999969 assigned positive charge : 379.1896 centred at (gu) : 98.94427 91.79211 89.99741 assigned negative charge : -379.6906 centred at (gu) : 98.88136 91.16518 89.99345 start vw surface at 0.2100000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 158140 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25657 grid for indexing accessible points = 1.400000 m= 74973 mr = 109980 m= 27127 mr = 58717 m= 6114 mr = 21062 m= 612 mr = 4448 m= 13 mr = 380 m= 0 mr = 0 time to grow re-entrant surface = 0.7500001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.350000 number of dielectric boundary points 72392 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 21200 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) : 1.742194 object centre at (A) : -1.655001 -10.39300 4.592001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1338742 -0.1067287 midg,1,midg; midg,igrid,midg -3.5224864E-03 9.5490858E-02 1,midg,midg; igrid,midg,midg 7.9686660E-03 -9.7242398E-03 gauss-seidel spectral radius is 0.9992037 estimated iterations to convergence 280 setup time was (sec) 1.660000 now iterating at: 08:55:46 rms-change max change #iterations 8.688027 277.8586 at 10iterations 5.008319 136.0694 at 20iterations 2.882608 63.44338 at 30iterations 1.646015 37.45881 at 40iterations 0.9370496 19.62811 at 50iterations 0.5323343 10.68244 at 60iterations 0.3015059 6.216124 at 70iterations 0.1705219 3.281853 at 80iterations 9.6454956E-02 2.069736 at 90iterations 5.4552790E-02 1.131697 at 100iterations 3.0861313E-02 0.6372490 at 110iterations 1.7485205E-02 0.3423748 at 120iterations 9.9562686E-03 0.1948700 at 130iterations 5.7721804E-03 0.1319542 at 140iterations 3.4283518E-03 7.8674316E-02 at 150iterations 2.1370654E-03 5.0636292E-02 at 160iterations 1.4278260E-03 3.3002853E-02 at 170iterations 1.0330799E-03 2.4851799E-02 at 180iterations finished qdiffx linear iterations at : 08:55:58 total time elapsed so far: 13.84000 # loops : 180 mean,max change (kT/e) : 1.0330799E-03 2.4851799E-02 energy calculations done at 13.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.05000 DelPhi exited at 08:55:59 14.048u 0.213s 0:14.63 97.4% 0+0k 0+0io 0pf+0w