Sat Oct 15 11:47:01 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 15 2011 at 11:47:02 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 = 2227 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: 0.6518952 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): -15.51900 27.88900 ymin,ymax (A): -11.77800 41.80300 zmin,zma (A): 0.3530000 54.96300 x,y,z range (A): 43.40800 53.58100 54.61000 scale (grids/A): 0.6518952 object centre (A): 6.185000 15.01250 27.65800 number of atom coordinates read : 2227 total number of charged atoms : 2093 net assigned charge : 11.00003 assigned positive charge : 323.2138 centred at (gu) : 88.57371 91.36925 88.82236 assigned negative charge : -312.2143 centred at (gu) : 88.67535 91.37748 88.82490 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6554 nv = 96 ne = 84 npr = 44416 no. pairs analyzed = 44416 no. exposed pairs = 3041 no. arc points = 21683 no. surface atoms = 1010 nbur = 1217 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 413 mr = 3362 m= 4 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3559 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2133 ## 206 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7676 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8509250E-08 1.7168428E-08 midg,1,midg; midg,igrid,midg 1.7556319E-08 2.7796764E-08 1,midg,midg; igrid,midg,midg 4.7131543E-08 6.8480190E-09 gauss-seidel spectral radius is 0.9877825 estimated iterations to convergence 74 setup time was (sec) 0.4000000 now iterating at: 11:47:02 rms-change max change #iterations 0.1437178 23.32667 at 10iterations 1.4813629E-02 2.279816 at 20iterations 1.5307092E-03 0.2010155 at 30iterations 1.6870098E-04 2.4404526E-02 at 40iterations 2.3539838E-05 3.5858154E-03 at 50iterations finished qdiffx linear iterations at : 11:47:05 total time elapsed so far: 3.600000 # loops : 50 mean,max change (kT/e) : 2.3539838E-05 3.5858154E-03 energy calculations done at 3.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.740000 DelPhi exited at 11:47:06 3.742u 0.206s 0:04.32 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 Sat Oct 15 2011 at 11:47:06 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2227 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: 1.955686 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): -15.51900 27.88900 ymin,ymax (A): -11.77800 41.80300 zmin,zma (A): 0.3530000 54.96300 x,y,z range (A): 43.40800 53.58100 54.61000 scale (grids/A): 1.955686 object centre (A): 6.185000 15.01250 27.65800 number of atom coordinates read : 2227 total number of charged atoms : 2093 net assigned charge : 11.00003 assigned positive charge : 323.2138 centred at (gu) : 85.72102 94.10776 86.46694 assigned negative charge : -312.2143 centred at (gu) : 86.02613 94.13253 86.47496 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 69922 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21683 grid for indexing accessible points = 1.400000 m= 25598 mr = 46491 m= 4636 mr = 18194 m= 345 mr = 2779 m= 8 mr = 145 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 32900 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 134 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 16523 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) : 0.6518952 object centre at (A) : 6.185000 15.01250 27.65800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7153789E-02 3.9190758E-02 midg,1,midg; midg,igrid,midg 5.0438978E-02 2.7012078E-02 1,midg,midg; igrid,midg,midg 3.3115882E-02 -3.6802737E-03 gauss-seidel spectral radius is 0.9986747 estimated iterations to convergence 218 setup time was (sec) 0.6200000 now iterating at: 11:47:07 rms-change max change #iterations 3.977573 181.9048 at 10iterations 1.878472 65.51418 at 20iterations 0.8867595 33.21155 at 30iterations 0.4207969 14.02166 at 40iterations 0.1983397 6.325479 at 50iterations 9.3834907E-02 3.233212 at 60iterations 4.4395439E-02 1.482166 at 70iterations 2.1026641E-02 0.7396545 at 80iterations 9.9581499E-03 0.4050274 at 90iterations 4.6919887E-03 0.1560516 at 100iterations 2.2279606E-03 7.6868057E-02 at 110iterations 1.0632441E-03 3.7269592E-02 at 120iterations finished qdiffx linear iterations at : 11:47:14 total time elapsed so far: 8.370000 # loops : 120 mean,max change (kT/e) : 1.0632441E-03 3.7269592E-02 energy calculations done at 8.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.500000 DelPhi exited at 11:47:15 8.506u 0.251s 0:09.30 94.0% 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 15 2011 at 11:47:15 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 = 2227 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: 2.933529 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): -15.51900 27.88900 ymin,ymax (A): -11.77800 41.80300 zmin,zma (A): 0.3530000 54.96300 x,y,z range (A): 43.40800 53.58100 54.61000 scale (grids/A): 2.933529 object centre (A): 6.185000 15.01250 27.65800 number of atom coordinates read : 2227 total number of charged atoms : 2093 net assigned charge : 11.00003 assigned positive charge : 323.2138 centred at (gu) : 83.58160 96.16145 84.70045 assigned negative charge : -312.2143 centred at (gu) : 84.03930 96.19888 84.71256 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 161355 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21683 grid for indexing accessible points = 1.400000 m= 80911 mr = 112805 m= 30915 mr = 64670 m= 8410 mr = 24160 m= 1482 mr = 6236 m= 140 mr = 961 m= 2 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9700000 number of dielectric boundary points 74325 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 16744 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) : 1.955686 object centre at (A) : 6.185000 15.01250 27.65800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6433284 0.4266945 midg,1,midg; midg,igrid,midg 0.6947799 0.3088505 1,midg,midg; igrid,midg,midg 0.2871954 -3.8397845E-02 gauss-seidel spectral radius is 0.9992778 estimated iterations to convergence 294 setup time was (sec) 1.270000 now iterating at: 11:47:17 rms-change max change #iterations 9.513492 449.5742 at 10iterations 5.653125 153.2748 at 20iterations 3.331943 79.18026 at 30iterations 1.957974 46.29028 at 40iterations 1.148105 26.03803 at 50iterations 0.6708041 13.05145 at 60iterations 0.3913092 7.569468 at 70iterations 0.2270584 4.550578 at 80iterations 0.1320020 2.741922 at 90iterations 7.6883987E-02 1.495239 at 100iterations 4.4516210E-02 0.8522987 at 110iterations 2.5858371E-02 0.5187569 at 120iterations 1.4972948E-02 0.2904193 at 130iterations 8.6844526E-03 0.1730235 at 140iterations 5.0429008E-03 9.8426819E-02 at 150iterations 2.9225773E-03 5.2569389E-02 at 160iterations 1.7019330E-03 3.0847549E-02 at 170iterations 9.9293306E-04 1.8569946E-02 at 180iterations finished qdiffx linear iterations at : 11:47:31 total time elapsed so far: 14.75000 # loops : 180 mean,max change (kT/e) : 9.9293306E-04 1.8569946E-02 energy calculations done at 14.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.89000 DelPhi exited at 11:47:32 14.888u 0.277s 0:16.35 92.6% 0+0k 0+0io 0pf+0w