Tue Oct 11 08:19:54 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 08:19:54 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1152 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: 0.7430443 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): -6.467000 32.10100 ymin,ymax (A): 1.376000 40.08000 zmin,zma (A): -1.535000 46.37600 x,y,z range (A): 38.56800 38.70400 47.91100 scale (grids/A): 0.7430443 object centre (A): 12.81700 20.72800 22.42050 number of atom coordinates read : 1152 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 88.62103 89.29262 88.43372 assigned negative charge : -169.8232 centred at (gu) : 88.30971 89.23788 88.46326 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4315 nv = 96 ne = 84 npr = 22015 no. pairs analyzed = 22015 no. exposed pairs = 1517 no. arc points = 11011 no. surface atoms = 513 nbur = 639 mkacc time = 3.9999999E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 298 mr = 2205 m= 1 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 3.9999999E-02 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.1200000 number of dielectric boundary points 2353 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 927 ## 81 charges are in solution ## iepsmp to db, and charging done at 0.1900000 number of grid points assigned charge 4488 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6368131E-07 6.7714133E-08 midg,1,midg; midg,igrid,midg 8.4583959E-08 1.2060967E-07 1,midg,midg; igrid,midg,midg -1.0261120E-07 2.1571603E-07 gauss-seidel spectral radius is 0.9904633 estimated iterations to convergence 83 setup time was (sec) 0.3100000 now iterating at: 08:19:54 rms-change max change #iterations 0.1744116 26.39516 at 10iterations 2.3272181E-02 4.241943 at 20iterations 3.1446032E-03 0.5448570 at 30iterations 4.1866544E-04 7.1651459E-02 at 40iterations 5.4293410E-05 9.3870163E-03 at 50iterations finished qdiffx linear iterations at : 08:19:57 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 5.4293410E-05 9.3870163E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 08:19:58 3.303u 0.172s 0:03.92 88.5% 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 08:19:58 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1152 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: 2.229133 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): -6.467000 32.10100 ymin,ymax (A): 1.376000 40.08000 zmin,zma (A): -1.535000 46.37600 x,y,z range (A): 38.56800 38.70400 47.91100 scale (grids/A): 2.229133 object centre (A): 12.81700 20.72800 22.42050 number of atom coordinates read : 1152 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 85.86317 87.87802 85.30113 assigned negative charge : -169.8232 centred at (gu) : 84.92926 87.71381 85.39002 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 45178 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11011 grid for indexing accessible points = 1.400000 m= 17020 mr = 29276 m= 3291 mr = 12637 m= 324 mr = 2208 m= 13 mr = 178 m= 0 mr = 8 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 604 time to turn everything in is 0.2600000 number of dielectric boundary points 21519 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 41 iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 8451 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) : 0.7430443 object centre at (A) : 12.81700 20.72800 22.42050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7411567E-02 9.6867569E-03 midg,1,midg; midg,igrid,midg 3.8582407E-02 3.7298631E-02 1,midg,midg; igrid,midg,midg -3.2104142E-02 3.8400996E-02 gauss-seidel spectral radius is 0.9988398 estimated iterations to convergence 232 setup time was (sec) 0.4700000 now iterating at: 08:19:59 rms-change max change #iterations 3.582747 208.2421 at 10iterations 1.775071 78.39616 at 20iterations 0.8810685 38.87347 at 30iterations 0.4392650 17.78504 at 40iterations 0.2158326 8.504944 at 50iterations 0.1071410 3.854670 at 60iterations 5.2972332E-02 2.066872 at 70iterations 2.6435247E-02 0.9953206 at 80iterations 1.3040070E-02 0.4701242 at 90iterations 6.4606443E-03 0.2405815 at 100iterations 3.1984812E-03 0.1385536 at 110iterations 1.5813499E-03 5.6877613E-02 at 120iterations finished qdiffx linear iterations at : 08:20:05 total time elapsed so far: 7.330000 # loops : 120 mean,max change (kT/e) : 1.5813499E-03 5.6877613E-02 energy calculations done at 7.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 08:20:06 7.462u 0.175s 0:08.11 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 Tue Oct 11 2011 at 08:20:06 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1152 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: 3.343699 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): -6.467000 32.10100 ymin,ymax (A): 1.376000 40.08000 zmin,zma (A): -1.535000 46.37600 x,y,z range (A): 38.56800 38.70400 47.91100 scale (grids/A): 3.343699 object centre (A): 12.81700 20.72800 22.42050 number of atom coordinates read : 1152 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 83.79482 86.81718 82.95168 assigned negative charge : -169.8232 centred at (gu) : 82.39393 86.57076 83.08511 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 103984 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11011 grid for indexing accessible points = 1.400000 m= 52394 mr = 70792 m= 21564 mr = 42607 m= 6202 mr = 17806 m= 1266 mr = 4830 m= 202 mr = 977 m= 27 mr = 143 m= 0 mr = 23 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1963 time to turn everything in is 0.7100000 number of dielectric boundary points 48461 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 8488 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) : 2.229133 object centre at (A) : 12.81700 20.72800 22.42050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2814060 0.1458515 midg,1,midg; midg,igrid,midg 0.3726663 0.3119054 1,midg,midg; igrid,midg,midg -0.2603771 0.2720576 gauss-seidel spectral radius is 0.9992966 estimated iterations to convergence 297 setup time was (sec) 0.9400000 now iterating at: 08:20:07 rms-change max change #iterations 7.914269 317.0937 at 10iterations 4.619288 134.9307 at 20iterations 2.687073 56.69536 at 30iterations 1.552764 36.87560 at 40iterations 0.9050862 20.06123 at 50iterations 0.5243258 11.39064 at 60iterations 0.3043101 6.607250 at 70iterations 0.1768144 3.879382 at 80iterations 0.1026504 2.247845 at 90iterations 5.9424367E-02 1.235811 at 100iterations 3.4514513E-02 0.7278414 at 110iterations 2.0020070E-02 0.4144096 at 120iterations 1.1655698E-02 0.2656136 at 130iterations 6.7602843E-03 0.1489449 at 140iterations 3.9171199E-03 8.1268311E-02 at 150iterations 2.2727244E-03 4.9009323E-02 at 160iterations 1.3228623E-03 2.9617310E-02 at 170iterations 7.6834788E-04 1.6588211E-02 at 180iterations finished qdiffx linear iterations at : 08:20:18 total time elapsed so far: 11.76000 # loops : 180 mean,max change (kT/e) : 7.6834788E-04 1.6588211E-02 energy calculations done at 11.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.90000 DelPhi exited at 08:20:18 11.898u 0.197s 0:12.38 97.5% 0+0k 0+0io 0pf+0w