Tue Oct 11 08:19:55 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 Tue Oct 11 2011 at 08:19:55 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 = 2757 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6351245 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): -5.265000 50.78700 ymin,ymax (A): -16.09400 29.59900 zmin,zma (A): 57.61900 109.4130 x,y,z range (A): 56.05200 45.69300 51.79400 scale (grids/A): 0.6351245 object centre (A): 22.76100 6.752501 83.51600 number of atom coordinates read : 2757 total number of charged atoms : 2613 net assigned charge : 5.500018 assigned positive charge : 416.1975 centred at (gu) : 90.07619 90.15648 89.50076 assigned negative charge : -410.6982 centred at (gu) : 90.31896 90.07838 89.55434 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7420 nv = 96 ne = 84 npr = 55859 no. pairs analyzed = 55859 no. exposed pairs = 3226 no. arc points = 22709 no. surface atoms = 1093 nbur = 1664 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 392 mr = 4249 m= 2 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 95 time to turn everything in is 0.3300000 number of dielectric boundary points 3507 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2186 ## 205 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8920 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4158961E-08 1.0663839E-09 midg,1,midg; midg,igrid,midg -1.4738112E-09 1.5857829E-08 1,midg,midg; igrid,midg,midg 3.1974416E-08 -2.0310937E-08 gauss-seidel spectral radius is 0.9871684 estimated iterations to convergence 72 setup time was (sec) 0.6300000 now iterating at: 08:19:56 rms-change max change #iterations 0.1471276 24.73828 at 10iterations 1.4820563E-02 2.218784 at 20iterations 2.1231580E-03 0.3833008 at 30iterations 5.5533624E-04 0.1197395 at 40iterations 1.7304921E-04 3.8341522E-02 at 50iterations finished qdiffx linear iterations at : 08:20:01 total time elapsed so far: 4.950000 # loops : 50 mean,max change (kT/e) : 1.7304921E-04 3.8341522E-02 energy calculations done at 4.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.130000 DelPhi exited at 08:20:02 5.133u 0.406s 0:06.42 86.1% 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 Tue Oct 11 2011 at 08:20:02 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 = 2757 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.905374 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): -5.265000 50.78700 ymin,ymax (A): -16.09400 29.59900 zmin,zma (A): 57.61900 109.4130 x,y,z range (A): 56.05200 45.69300 51.79400 scale (grids/A): 1.905374 object centre (A): 22.76100 6.752501 83.51600 number of atom coordinates read : 2757 total number of charged atoms : 2613 net assigned charge : 5.500018 assigned positive charge : 416.1975 centred at (gu) : 90.22796 90.46878 88.50130 assigned negative charge : -410.6982 centred at (gu) : 90.95683 90.23489 88.66268 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 80573 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22709 grid for indexing accessible points = 1.400000 m= 29096 mr = 57000 m= 4387 mr = 21854 m= 259 mr = 2868 m= 2 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 3710 time to turn everything in is 0.6600000 number of dielectric boundary points 32491 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 153 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 20544 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) : 0.6351245 object centre at (A) : 22.76100 6.752501 83.51600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.9689884E-03 6.6870805E-03 midg,1,midg; midg,igrid,midg 1.3650693E-02 2.1543387E-02 1,midg,midg; igrid,midg,midg 4.6937946E-02 -3.8907126E-02 gauss-seidel spectral radius is 0.9986480 estimated iterations to convergence 216 setup time was (sec) 1.030000 now iterating at: 08:20:03 rms-change max change #iterations 4.392604 174.1965 at 10iterations 2.057970 66.14767 at 20iterations 0.9671726 29.00459 at 30iterations 0.4539993 15.27279 at 40iterations 0.2135853 6.330627 at 50iterations 0.1006508 3.414768 at 60iterations 4.7510136E-02 1.386469 at 70iterations 2.2514237E-02 0.7229404 at 80iterations 1.0721698E-02 0.3494720 at 90iterations 5.1812669E-03 0.1749687 at 100iterations 2.5732548E-03 9.7274780E-02 at 110iterations 1.3419804E-03 4.8141479E-02 at 120iterations finished qdiffx linear iterations at : 08:20:14 total time elapsed so far: 11.59000 # loops : 120 mean,max change (kT/e) : 1.3419804E-03 4.8141479E-02 energy calculations done at 11.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.76000 DelPhi exited at 08:20:15 11.760u 0.482s 0:12.96 94.4% 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 Tue Oct 11 2011 at 08:20:15 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 = 2757 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.858060 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): -5.265000 50.78700 ymin,ymax (A): -16.09400 29.59900 zmin,zma (A): 57.61900 109.4130 x,y,z range (A): 56.05200 45.69300 51.79400 scale (grids/A): 2.858060 object centre (A): 22.76100 6.752501 83.51600 number of atom coordinates read : 2757 total number of charged atoms : 2613 net assigned charge : 5.500018 assigned positive charge : 416.1975 centred at (gu) : 90.34167 90.70299 87.75192 assigned negative charge : -410.6982 centred at (gu) : 91.43515 90.35225 87.99395 start vw surface at 0.1300000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 186649 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22709 grid for indexing accessible points = 1.400000 m= 94642 mr = 137832 m= 33660 mr = 78536 m= 8033 mr = 27445 m= 1179 mr = 6269 m= 64 mr = 854 m= 0 mr = 14 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 12193 time to turn everything in is 1.780000 number of dielectric boundary points 73277 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 20900 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) : 1.905374 object centre at (A) : 22.76100 6.752501 83.51600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.3086560E-02 1.1511606E-02 midg,1,midg; midg,igrid,midg 0.2042612 0.2279392 1,midg,midg; igrid,midg,midg 0.5563724 -0.2537593 gauss-seidel spectral radius is 0.9992575 estimated iterations to convergence 290 setup time was (sec) 2.160000 now iterating at: 08:20:18 rms-change max change #iterations 10.16949 337.5100 at 10iterations 5.905537 147.3457 at 20iterations 3.418662 68.31628 at 30iterations 1.972172 35.87383 at 40iterations 1.134920 25.08263 at 50iterations 0.6556086 12.44780 at 60iterations 0.3762590 7.011303 at 70iterations 0.2162196 4.048225 at 80iterations 0.1242588 2.125099 at 90iterations 7.1376577E-02 1.409226 at 100iterations 4.1163065E-02 0.7028885 at 110iterations 2.3732537E-02 0.4039459 at 120iterations 1.3696110E-02 0.2879028 at 130iterations 7.9705259E-03 0.1447906 at 140iterations 4.7081630E-03 9.8308563E-02 at 150iterations 2.8336372E-03 5.6152344E-02 at 160iterations 1.7701351E-03 4.5219421E-02 at 170iterations 1.1688629E-03 2.7492523E-02 at 180iterations finished qdiffx linear iterations at : 08:20:35 total time elapsed so far: 19.46000 # loops : 180 mean,max change (kT/e) : 1.1688629E-03 2.7492523E-02 energy calculations done at 19.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.62000 DelPhi exited at 08:20:36 19.626u 0.611s 0:20.92 96.7% 0+0k 0+0io 0pf+0w