Mon Oct 10 10:19:10 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 Mon Oct 10 2011 at 10:19:10 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 = 2801 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: 0.5771164 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): -21.84500 39.84100 ymin,ymax (A): -12.36300 43.70400 zmin,zma (A): -1.375000 51.34200 x,y,z range (A): 61.68600 56.06700 52.71700 scale (grids/A): 0.5771164 object centre (A): 8.998000 15.67050 24.98350 number of atom coordinates read : 2801 total number of charged atoms : 2655 net assigned charge : 12.00002 assigned positive charge : 410.7710 centred at (gu) : 92.02052 91.84340 86.84414 assigned negative charge : -398.7714 centred at (gu) : 92.11701 91.88406 86.63936 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6376 nv = 96 ne = 84 npr = 53684 no. pairs analyzed = 53684 no. exposed pairs = 4084 no. arc points = 29928 no. surface atoms = 1355 nbur = 1446 mkacc time = 0.1200000 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 = 1.484000 m= 323 mr = 2875 m= 0 mr = 13 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3811 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2993 ## 329 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8032 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7178819E-09 2.9030154E-09 midg,1,midg; midg,igrid,midg 2.1098445E-09 2.7183482E-09 1,midg,midg; igrid,midg,midg 2.6235694E-09 1.2098936E-09 gauss-seidel spectral radius is 0.9845074 estimated iterations to convergence 66 setup time was (sec) 0.5300000 now iterating at: 10:19:11 rms-change max change #iterations 9.0473101E-02 17.86728 at 10iterations 6.9009629E-03 1.148193 at 20iterations 5.4973742E-04 8.2687378E-02 at 30iterations 4.8698050E-05 7.5016022E-03 at 40iterations 6.4228097E-06 8.4495544E-04 at 50iterations finished qdiffx linear iterations at : 10:19:13 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 6.4228097E-06 8.4495544E-04 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 10:19:14 3.286u 0.166s 0:03.76 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 Mon Oct 10 2011 at 10:19:14 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 = 2801 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.731349 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): -21.84500 39.84100 ymin,ymax (A): -12.36300 43.70400 zmin,zma (A): -1.375000 51.34200 x,y,z range (A): 61.68600 56.06700 52.71700 scale (grids/A): 1.731349 object centre (A): 8.998000 15.67050 24.98350 number of atom coordinates read : 2801 total number of charged atoms : 2655 net assigned charge : 12.00002 assigned positive charge : 410.7710 centred at (gu) : 96.06075 95.52968 80.53185 assigned negative charge : -398.7714 centred at (gu) : 96.35078 95.65195 79.91779 start vw surface at 0.1900000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 68270 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29928 grid for indexing accessible points = 1.400000 m= 22375 mr = 42404 m= 2965 mr = 14687 m= 116 mr = 1382 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 35241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 252 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 20618 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) : 0.5771164 object centre at (A) : 8.998000 15.67050 24.98350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.6631532E-04 1.3799111E-02 midg,1,midg; midg,igrid,midg 1.8300584E-02 2.8268259E-02 1,midg,midg; igrid,midg,midg -6.8487157E-03 1.1581934E-02 gauss-seidel spectral radius is 0.9983840 estimated iterations to convergence 197 setup time was (sec) 0.7900000 now iterating at: 10:19:15 rms-change max change #iterations 3.516909 145.4652 at 10iterations 1.515878 65.09595 at 20iterations 0.6621205 23.84465 at 30iterations 0.2893603 9.829819 at 40iterations 0.1258113 4.324089 at 50iterations 5.5137530E-02 1.871758 at 60iterations 2.3988951E-02 0.8939781 at 70iterations 1.0484912E-02 0.3804264 at 80iterations 4.5709852E-03 0.1625376 at 90iterations 2.0049911E-03 7.6339722E-02 at 100iterations 8.7639154E-04 3.4260750E-02 at 110iterations 3.8415202E-04 1.4529705E-02 at 120iterations finished qdiffx linear iterations at : 10:19:21 total time elapsed so far: 6.790000 # loops : 120 mean,max change (kT/e) : 3.8415202E-04 1.4529705E-02 energy calculations done at 6.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.970000 DelPhi exited at 10:19:22 6.969u 0.169s 0:07.47 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 10:19:22 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 = 2801 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.597024 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): -21.84500 39.84100 ymin,ymax (A): -12.36300 43.70400 zmin,zma (A): -1.375000 51.34200 x,y,z range (A): 61.68600 56.06700 52.71700 scale (grids/A): 2.597024 object centre (A): 8.998000 15.67050 24.98350 number of atom coordinates read : 2801 total number of charged atoms : 2655 net assigned charge : 12.00002 assigned positive charge : 410.7710 centred at (gu) : 99.09107 98.29443 75.79774 assigned negative charge : -398.7714 centred at (gu) : 99.52625 98.47786 74.87663 start vw surface at 0.1700000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 158024 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29928 grid for indexing accessible points = 1.400000 m= 72882 mr = 104751 m= 24392 mr = 55433 m= 4792 mr = 17695 m= 410 mr = 2973 m= 20 mr = 163 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.230000 number of dielectric boundary points 79505 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 21230 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) : 1.731349 object centre at (A) : 8.998000 15.67050 24.98350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2217788E-03 0.1459637 midg,1,midg; midg,igrid,midg 0.2973661 0.3409154 1,midg,midg; igrid,midg,midg -0.3393249 0.2160290 gauss-seidel spectral radius is 0.9992020 estimated iterations to convergence 280 setup time was (sec) 1.510000 now iterating at: 10:19:23 rms-change max change #iterations 9.116270 290.6016 at 10iterations 5.330672 153.2405 at 20iterations 3.071113 87.09094 at 30iterations 1.763520 61.94933 at 40iterations 1.006453 24.36760 at 50iterations 0.5729028 14.59008 at 60iterations 0.3250022 7.903476 at 70iterations 0.1840616 4.057371 at 80iterations 0.1038239 2.215724 at 90iterations 5.8616485E-02 1.347508 at 100iterations 3.3072986E-02 0.6578703 at 110iterations 1.8668536E-02 0.4535232 at 120iterations 1.0516699E-02 0.2115178 at 130iterations 5.9096301E-03 0.1280670 at 140iterations 3.3240682E-03 7.8159332E-02 at 150iterations 1.8714208E-03 4.1275978E-02 at 160iterations 1.0556228E-03 2.1488190E-02 at 170iterations 5.9299485E-04 1.1491776E-02 at 180iterations finished qdiffx linear iterations at : 10:19:33 total time elapsed so far: 11.00000 # loops : 180 mean,max change (kT/e) : 5.9299485E-04 1.1491776E-02 energy calculations done at 11.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.20000 DelPhi exited at 10:19:33 11.206u 0.214s 0:11.69 97.6% 0+0k 0+0io 0pf+0w