Sat Oct 8 23:50:26 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+sph.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 Sat Oct 8 2011 at 23:50:26 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2173 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6640800 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): -26.99500 26.61300 ymin,ymax (A): -15.41400 27.88800 zmin,zma (A): -3.546000 49.39800 x,y,z range (A): 53.60800 43.30200 52.94400 scale (grids/A): 0.6640800 object centre (A): -0.1910009 6.237000 22.92600 number of atom coordinates read : 2173 total number of charged atoms : 2039 net assigned charge : 11.50002 assigned positive charge : 316.4868 centred at (gu) : 90.62141 88.88756 88.46663 assigned negative charge : -304.9872 centred at (gu) : 90.61043 88.93816 88.43240 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7087 nv = 96 ne = 84 npr = 41141 no. pairs analyzed = 41141 no. exposed pairs = 3124 no. arc points = 22507 no. surface atoms = 1025 nbur = 1148 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 501 mr = 3661 m= 1 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3847 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2106 ## 202 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7742 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.6027490E-08 2.8241130E-08 midg,1,midg; midg,igrid,midg 5.1556746E-08 1.9133930E-08 1,midg,midg; igrid,midg,midg 2.7047545E-08 3.8928462E-08 gauss-seidel spectral radius is 0.9882286 estimated iterations to convergence 75 setup time was (sec) 0.6500000 now iterating at: 23:50:27 rms-change max change #iterations 0.1507268 23.28898 at 10iterations 1.6248720E-02 2.260025 at 20iterations 1.7402982E-03 0.2438393 at 30iterations 1.9069294E-04 2.5382996E-02 at 40iterations 2.1988333E-05 3.1433105E-03 at 50iterations finished qdiffx linear iterations at : 23:50:31 total time elapsed so far: 4.400000 # loops : 50 mean,max change (kT/e) : 2.1988333E-05 3.1433105E-03 energy calculations done at 4.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.560000 DelPhi exited at 23:50:31 4.563u 0.389s 0:05.24 94.2% 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 Sat Oct 8 2011 at 23:50:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2173 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.992240 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): -26.99500 26.61300 ymin,ymax (A): -15.41400 27.88800 zmin,zma (A): -3.546000 49.39800 x,y,z range (A): 53.60800 43.30200 52.94400 scale (grids/A): 1.992240 object centre (A): -0.1910009 6.237000 22.92600 number of atom coordinates read : 2173 total number of charged atoms : 2039 net assigned charge : 11.50002 assigned positive charge : 316.4868 centred at (gu) : 91.86404 86.66265 85.39963 assigned negative charge : -304.9872 centred at (gu) : 91.83157 86.81446 85.29738 start vw surface at 0.1100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 74244 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22507 grid for indexing accessible points = 1.400000 m= 29942 mr = 48999 m= 6144 mr = 21947 m= 517 mr = 3974 m= 5 mr = 248 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 35684 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 16095 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) : 0.6640800 object centre at (A) : -0.1910009 6.237000 22.92600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2830436E-02 6.1052170E-02 midg,1,midg; midg,igrid,midg 2.7594676E-02 -1.0639406E-03 1,midg,midg; igrid,midg,midg 5.5388927E-02 6.2708922E-02 gauss-seidel spectral radius is 0.9987285 estimated iterations to convergence 222 setup time was (sec) 0.9400000 now iterating at: 23:50:33 rms-change max change #iterations 4.088562 193.5621 at 10iterations 1.950267 67.98071 at 20iterations 0.9363109 29.69339 at 30iterations 0.4480686 16.57046 at 40iterations 0.2142737 6.538650 at 50iterations 0.1033605 3.507549 at 60iterations 4.9472690E-02 1.553438 at 70iterations 2.3806073E-02 0.7605000 at 80iterations 1.1453328E-02 0.3675795 at 90iterations 5.4923771E-03 0.1754646 at 100iterations 2.6420415E-03 7.6836586E-02 at 110iterations 1.2648520E-03 4.0525436E-02 at 120iterations finished qdiffx linear iterations at : 23:50:43 total time elapsed so far: 11.13000 # loops : 120 mean,max change (kT/e) : 1.2648520E-03 4.0525436E-02 energy calculations done at 11.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.30000 DelPhi exited at 23:50:43 11.306u 0.434s 0:11.99 97.8% 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 8 2011 at 23:50:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2173 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.988360 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): -26.99500 26.61300 ymin,ymax (A): -15.41400 27.88800 zmin,zma (A): -3.546000 49.39800 x,y,z range (A): 53.60800 43.30200 52.94400 scale (grids/A): 2.988360 object centre (A): -0.1910009 6.237000 22.92600 number of atom coordinates read : 2173 total number of charged atoms : 2039 net assigned charge : 11.50002 assigned positive charge : 316.4868 centred at (gu) : 92.79606 84.99388 83.09969 assigned negative charge : -304.9872 centred at (gu) : 92.74735 85.22186 82.94611 start vw surface at 0.1100000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 170837 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22507 grid for indexing accessible points = 1.400000 m= 91221 mr = 118763 m= 38851 mr = 73898 m= 11511 mr = 31287 m= 2219 mr = 8705 m= 205 mr = 1588 m= 3 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.670000 number of dielectric boundary points 80481 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 16304 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) : 1.992240 object centre at (A) : -0.1910009 6.237000 22.92600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3470925 0.8559877 midg,1,midg; midg,igrid,midg 0.2077214 -1.4765310E-02 1,midg,midg; igrid,midg,midg 0.5715091 0.5268213 gauss-seidel spectral radius is 0.9992968 estimated iterations to convergence 298 setup time was (sec) 2.020000 now iterating at: 23:50:46 rms-change max change #iterations 9.650245 419.7966 at 10iterations 5.777263 147.1463 at 20iterations 3.439753 83.66182 at 30iterations 2.038618 44.80565 at 40iterations 1.203974 25.97938 at 50iterations 0.7084650 14.39646 at 60iterations 0.4163129 9.390320 at 70iterations 0.2447958 4.847965 at 80iterations 0.1432323 3.137867 at 90iterations 8.3671004E-02 1.599744 at 100iterations 4.8997886E-02 0.9753609 at 110iterations 2.8602859E-02 0.5908089 at 120iterations 1.6662389E-02 0.3055289 at 130iterations 9.7365128E-03 0.1775608 at 140iterations 5.6708409E-03 0.1044769 at 150iterations 3.3153596E-03 6.3377619E-02 at 160iterations 1.9320698E-03 3.2431126E-02 at 170iterations 1.1278717E-03 2.1320343E-02 at 180iterations finished qdiffx linear iterations at : 23:51:02 total time elapsed so far: 18.61000 # loops : 180 mean,max change (kT/e) : 1.1278717E-03 2.1320343E-02 energy calculations done at 18.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.77000 DelPhi exited at 23:51:03 18.771u 0.449s 0:19.50 98.5% 0+0k 0+0io 0pf+0w