Tue Oct 11 06:01:28 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 06:01:28 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2281 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.7346568 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): 25.62500 72.11100 ymin,ymax (A): -18.59700 29.86100 zmin,zma (A): 4.167000 46.30400 x,y,z range (A): 46.48600 48.45800 42.13700 scale (grids/A): 0.7346568 object centre (A): 48.86800 5.632000 25.23550 number of atom coordinates read : 2281 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 89.17817 90.50719 90.19273 assigned negative charge : -311.0742 centred at (gu) : 89.31656 90.45139 90.27691 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7799 nv = 96 ne = 84 npr = 41617 no. pairs analyzed = 41617 no. exposed pairs = 2585 no. arc points = 17640 no. surface atoms = 881 nbur = 1400 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 606 mr = 4588 m= 6 mr = 133 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 0.3000000 number of dielectric boundary points 3690 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1534 ## 152 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8230 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6850676E-07 2.6455854E-08 midg,1,midg; midg,igrid,midg 4.6964409E-08 1.6469504E-07 1,midg,midg; igrid,midg,midg 2.5874667E-07 -1.9003988E-08 gauss-seidel spectral radius is 0.9903375 estimated iterations to convergence 83 setup time was (sec) 0.5700000 now iterating at: 06:01:29 rms-change max change #iterations 0.2322076 37.53531 at 10iterations 3.1149752E-02 3.853798 at 20iterations 4.5514461E-03 0.5483513 at 30iterations 8.2935317E-04 0.1076202 at 40iterations 2.3291394E-04 2.7664185E-02 at 50iterations finished qdiffx linear iterations at : 06:01:32 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 2.3291394E-04 2.7664185E-02 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.650000 DelPhi exited at 06:01:33 3.649u 0.187s 0:04.79 79.7% 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 06:01:33 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2281 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.203970 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): 25.62500 72.11100 ymin,ymax (A): -18.59700 29.86100 zmin,zma (A): 4.167000 46.30400 x,y,z range (A): 46.48600 48.45800 42.13700 scale (grids/A): 2.203970 object centre (A): 48.86800 5.632000 25.23550 number of atom coordinates read : 2281 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 87.53426 91.52161 90.57835 assigned negative charge : -311.0742 centred at (gu) : 87.95000 91.35427 90.83071 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 82062 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17640 grid for indexing accessible points = 1.400000 m= 35271 mr = 58840 m= 7639 mr = 27286 m= 854 mr = 5330 m= 28 mr = 442 m= 0 mr = 9 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6800000 number of dielectric boundary points 33947 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 59 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 15605 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) : 0.7346568 object centre at (A) : 48.86800 5.632000 25.23550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7301218E-02 3.2723200E-02 midg,1,midg; midg,igrid,midg 5.5114709E-02 3.4753457E-02 1,midg,midg; igrid,midg,midg 5.1573209E-02 -6.1372820E-02 gauss-seidel spectral radius is 0.9989069 estimated iterations to convergence 239 setup time was (sec) 1.000000 now iterating at: 06:01:34 rms-change max change #iterations 4.920288 220.3158 at 10iterations 2.489898 79.49850 at 20iterations 1.267842 34.39815 at 30iterations 0.6438121 17.42665 at 40iterations 0.3258978 9.355633 at 50iterations 0.1658960 4.858961 at 60iterations 8.4490895E-02 2.298779 at 70iterations 4.3094698E-02 1.192137 at 80iterations 2.2023473E-02 0.7166700 at 90iterations 1.1343845E-02 0.3471107 at 100iterations 5.8559342E-03 0.1619148 at 110iterations 3.1073077E-03 9.0057373E-02 at 120iterations finished qdiffx linear iterations at : 06:01:41 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 3.1073077E-03 9.0057373E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 06:01:42 7.755u 0.217s 0:08.49 93.7% 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 06:01:42 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2281 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: 3.305956 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): 25.62500 72.11100 ymin,ymax (A): -18.59700 29.86100 zmin,zma (A): 4.167000 46.30400 x,y,z range (A): 46.48600 48.45800 42.13700 scale (grids/A): 3.305956 object centre (A): 48.86800 5.632000 25.23550 number of atom coordinates read : 2281 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 86.30151 92.28230 90.86752 assigned negative charge : -311.0742 centred at (gu) : 86.92493 92.03135 91.24596 start vw surface at 0.1500000 fill in re-entrant regions at 0.9200000 boundary points on vw surface= 188863 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17640 grid for indexing accessible points = 1.400000 m= 107214 mr = 141181 m= 47078 mr = 90168 m= 14746 mr = 39278 m= 3297 mr = 11775 m= 486 mr = 2428 m= 36 mr = 339 m= 0 mr = 9 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.130000 number of dielectric boundary points 76542 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.280000 number of grid points assigned charge 15688 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) : 2.203970 object centre at (A) : 48.86800 5.632000 25.23550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1185416 0.2729326 midg,1,midg; midg,igrid,midg 0.4014927 0.1750023 1,midg,midg; igrid,midg,midg 0.4944066 -0.6979828 gauss-seidel spectral radius is 0.9993169 estimated iterations to convergence 302 setup time was (sec) 2.470000 now iterating at: 06:01:44 rms-change max change #iterations 10.73945 319.0255 at 10iterations 6.417317 125.2868 at 20iterations 3.820129 75.47872 at 30iterations 2.277215 61.70855 at 40iterations 1.352217 23.74954 at 50iterations 0.8014007 14.15796 at 60iterations 0.4745149 9.238838 at 70iterations 0.2806594 4.825018 at 80iterations 0.1660020 2.830853 at 90iterations 9.8117091E-02 1.746893 at 100iterations 5.8064938E-02 1.004563 at 110iterations 3.4484718E-02 0.5625916 at 120iterations 2.0619972E-02 0.3715839 at 130iterations 1.2468773E-02 0.2105522 at 140iterations 7.7043376E-03 0.1377430 at 150iterations 4.9593793E-03 9.0663910E-02 at 160iterations 3.3571429E-03 6.2374115E-02 at 170iterations 2.4305906E-03 4.1961670E-02 at 180iterations finished qdiffx linear iterations at : 06:01:58 total time elapsed so far: 16.20000 # loops : 180 mean,max change (kT/e) : 2.4305906E-03 4.1961670E-02 energy calculations done at 16.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.39000 DelPhi exited at 06:01:59 16.391u 0.285s 0:17.25 96.6% 0+0k 0+0io 0pf+0w