Mon Oct 10 13:55:04 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 13:55:04 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1064 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7490321 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): -27.45200 10.37400 ymin,ymax (A): 1.420000 41.45000 zmin,zma (A): 10.83800 58.36600 x,y,z range (A): 37.82600 40.03000 47.52800 scale (grids/A): 0.7490321 object centre (A): -8.539000 21.43500 34.60200 number of atom coordinates read : 1064 total number of charged atoms : 938 net assigned charge : 1.500003 assigned positive charge : 150.6850 centred at (gu) : 91.71687 91.39344 91.67829 assigned negative charge : -149.1850 centred at (gu) : 91.54646 91.49653 91.37320 start vw surface at 5.9999999E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4245 nv = 96 ne = 84 npr = 21378 no. pairs analyzed = 21378 no. exposed pairs = 1657 no. arc points = 12238 no. surface atoms = 553 nbur = 511 mkacc time = 3.9999999E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 315 mr = 1921 m= 3 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 4.9999997E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1200000 number of dielectric boundary points 2598 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 954 ## 65 charges are in solution ## iepsmp to db, and charging done at 0.1800000 number of grid points assigned charge 4145 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0831541E-07 2.6865345E-07 midg,1,midg; midg,igrid,midg 6.6334223E-08 -4.0788166E-08 1,midg,midg; igrid,midg,midg -4.9977487E-08 1.6969491E-07 gauss-seidel spectral radius is 0.9906101 estimated iterations to convergence 84 setup time was (sec) 0.3000000 now iterating at: 13:55:04 rms-change max change #iterations 0.1736889 32.55936 at 10iterations 2.2999194E-02 4.577171 at 20iterations 3.1243560E-03 0.5546112 at 30iterations 4.2622344E-04 6.9110870E-02 at 40iterations 5.6540262E-05 1.0109901E-02 at 50iterations finished qdiffx linear iterations at : 13:55:07 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 5.6540262E-05 1.0109901E-02 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 13:55:08 3.315u 0.170s 0:04.03 86.3% 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 13:55:08 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1064 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.247097 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): -27.45200 10.37400 ymin,ymax (A): 1.420000 41.45000 zmin,zma (A): 10.83800 58.36600 x,y,z range (A): 37.82600 40.03000 47.52800 scale (grids/A): 2.247097 object centre (A): -8.539000 21.43500 34.60200 number of atom coordinates read : 1064 total number of charged atoms : 938 net assigned charge : 1.500003 assigned positive charge : 150.6850 centred at (gu) : 95.15068 94.18038 95.03493 assigned negative charge : -149.1850 centred at (gu) : 94.63937 94.48956 94.11955 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 43149 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12238 grid for indexing accessible points = 1.400000 m= 16725 mr = 25905 m= 3864 mr = 11739 m= 443 mr = 2466 m= 11 mr = 179 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 23903 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 7481 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) : 0.7490321 object centre at (A) : -8.539000 21.43500 34.60200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9291548E-03 5.5168152E-02 midg,1,midg; midg,igrid,midg 1.9579861E-02 6.6890074E-03 1,midg,midg; igrid,midg,midg -9.9792350E-03 3.0440674E-03 gauss-seidel spectral radius is 0.9988562 estimated iterations to convergence 234 setup time was (sec) 0.4500000 now iterating at: 13:55:09 rms-change max change #iterations 3.502422 244.0578 at 10iterations 1.734181 80.22318 at 20iterations 0.8630468 37.64214 at 30iterations 0.4274072 17.45879 at 40iterations 0.2130875 8.499428 at 50iterations 0.1064330 4.406222 at 60iterations 5.2729473E-02 2.018349 at 70iterations 2.6102090E-02 0.9679184 at 80iterations 1.2966636E-02 0.5220490 at 90iterations 6.4545381E-03 0.2346573 at 100iterations 3.2243363E-03 0.1240497 at 110iterations 1.5911582E-03 6.0656309E-02 at 120iterations finished qdiffx linear iterations at : 13:55:16 total time elapsed so far: 7.470000 # loops : 120 mean,max change (kT/e) : 1.5911582E-03 6.0656309E-02 energy calculations done at 7.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.600000 DelPhi exited at 13:55:16 7.598u 0.205s 0:08.41 92.6% 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 13:55:17 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1064 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.370645 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): -27.45200 10.37400 ymin,ymax (A): 1.420000 41.45000 zmin,zma (A): 10.83800 58.36600 x,y,z range (A): 37.82600 40.03000 47.52800 scale (grids/A): 3.370645 object centre (A): -8.539000 21.43500 34.60200 number of atom coordinates read : 1064 total number of charged atoms : 938 net assigned charge : 1.500003 assigned positive charge : 150.6850 centred at (gu) : 97.72599 96.27061 97.55246 assigned negative charge : -149.1850 centred at (gu) : 96.95905 96.73434 96.17934 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 98965 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12238 grid for indexing accessible points = 1.400000 m= 49628 mr = 63267 m= 22302 mr = 38602 m= 7417 mr = 17708 m= 1668 mr = 5574 m= 214 mr = 1080 m= 13 mr = 128 m= 1 mr = 1 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 0.7300000 number of dielectric boundary points 53848 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 7504 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) : 2.247097 object centre at (A) : -8.539000 21.43500 34.60200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.4786929E-03 0.4924168 midg,1,midg; midg,igrid,midg 0.1578933 4.5146186E-02 1,midg,midg; igrid,midg,midg -4.0376715E-02 -1.7989239E-02 gauss-seidel spectral radius is 0.9993063 estimated iterations to convergence 300 setup time was (sec) 0.9700000 now iterating at: 13:55:18 rms-change max change #iterations 7.802566 323.0746 at 10iterations 4.594574 135.2534 at 20iterations 2.717302 76.93011 at 30iterations 1.598116 42.23014 at 40iterations 0.9395370 23.90537 at 50iterations 0.5504990 13.00197 at 60iterations 0.3205714 8.065375 at 70iterations 0.1873886 5.388760 at 80iterations 0.1094977 2.542274 at 90iterations 6.3978322E-02 1.368907 at 100iterations 3.7402757E-02 0.8785448 at 110iterations 2.1772889E-02 0.4632902 at 120iterations 1.2712657E-02 0.3032351 at 130iterations 7.3995204E-03 0.1712418 at 140iterations 4.3209512E-03 9.8129272E-02 at 150iterations 2.5172730E-03 5.4302216E-02 at 160iterations 1.4694352E-03 3.6550522E-02 at 170iterations 8.5794326E-04 1.8398702E-02 at 180iterations finished qdiffx linear iterations at : 13:55:29 total time elapsed so far: 11.97000 # loops : 180 mean,max change (kT/e) : 8.5794326E-04 1.8398702E-02 energy calculations done at 11.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.11000 DelPhi exited at 13:55:29 12.112u 0.196s 0:12.89 95.4% 0+0k 0+0io 0pf+0w