Mon Oct 10 22:42:27 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 22:42:27 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2274 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6814440 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): -0.2010000 52.04100 ymin,ymax (A): -19.75100 22.62100 zmin,zma (A): -8.708000 39.67900 x,y,z range (A): 52.24200 42.37200 48.38700 scale (grids/A): 0.6814440 object centre (A): 25.92000 1.435000 15.48550 number of atom coordinates read : 2274 total number of charged atoms : 2146 net assigned charge : 1.000010 assigned positive charge : 340.6741 centred at (gu) : 90.51714 89.79145 90.01311 assigned negative charge : -339.6748 centred at (gu) : 90.72429 89.64055 90.31560 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7274 nv = 96 ne = 84 npr = 45515 no. pairs analyzed = 45515 no. exposed pairs = 2854 no. arc points = 20271 no. surface atoms = 957 nbur = 1317 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 449 mr = 4061 m= 5 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 32 time to turn everything in is 0.2700000 number of dielectric boundary points 3592 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1771 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8199 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.1386511E-08 -8.7059263E-08 midg,1,midg; midg,igrid,midg -4.1769070E-08 4.6937831E-08 1,midg,midg; igrid,midg,midg 5.8441525E-08 -6.3709408E-08 gauss-seidel spectral radius is 0.9888092 estimated iterations to convergence 77 setup time was (sec) 0.6000000 now iterating at: 22:42:28 rms-change max change #iterations 0.1838138 24.63811 at 10iterations 2.0447336E-02 2.840103 at 20iterations 2.3699841E-03 0.3176947 at 30iterations 2.6466927E-04 3.5465240E-02 at 40iterations 3.0189094E-05 3.9787292E-03 at 50iterations finished qdiffx linear iterations at : 22:42:32 total time elapsed so far: 5.010000 # loops : 50 mean,max change (kT/e) : 3.0189094E-05 3.9787292E-03 energy calculations done at 5.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.150000 DelPhi exited at 22:42:33 5.158u 0.466s 0:05.96 94.1% 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 Mon Oct 10 2011 at 22:42:33 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2274 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.044332 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): -0.2010000 52.04100 ymin,ymax (A): -19.75100 22.62100 zmin,zma (A): -8.708000 39.67900 x,y,z range (A): 52.24200 42.37200 48.38700 scale (grids/A): 2.044332 object centre (A): 25.92000 1.435000 15.48550 number of atom coordinates read : 2274 total number of charged atoms : 2146 net assigned charge : 1.000010 assigned positive charge : 340.6741 centred at (gu) : 91.55099 89.37394 90.03886 assigned negative charge : -339.6748 centred at (gu) : 92.17260 88.92139 90.94659 start vw surface at 0.1100000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 77757 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20271 grid for indexing accessible points = 1.400000 m= 29483 mr = 54090 m= 5379 mr = 22179 m= 472 mr = 3561 m= 11 mr = 212 m= 0 mr = 1 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 712 time to turn everything in is 0.6300000 number of dielectric boundary points 33059 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 81 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 17005 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) : 0.6814440 object centre at (A) : 25.92000 1.435000 15.48550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5552123E-02 -5.5077095E-02 midg,1,midg; midg,igrid,midg -1.2046146E-02 2.3488689E-02 1,midg,midg; igrid,midg,midg 5.4821582E-04 -8.9702293E-02 gauss-seidel spectral radius is 0.9987795 estimated iterations to convergence 227 setup time was (sec) 0.9800000 now iterating at: 22:42:34 rms-change max change #iterations 4.514992 171.8411 at 10iterations 2.206552 79.36479 at 20iterations 1.071779 33.97558 at 30iterations 0.5233156 15.13237 at 40iterations 0.2555266 9.010525 at 50iterations 0.1247278 4.504538 at 60iterations 6.0913023E-02 2.147190 at 70iterations 2.9642032E-02 0.8777719 at 80iterations 1.4461750E-02 0.4264641 at 90iterations 7.0460653E-03 0.2051811 at 100iterations 3.4392076E-03 0.1116495 at 110iterations 1.6820906E-03 5.5868149E-02 at 120iterations finished qdiffx linear iterations at : 22:42:45 total time elapsed so far: 11.89000 # loops : 120 mean,max change (kT/e) : 1.6820906E-03 5.5868149E-02 energy calculations done at 11.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.06000 DelPhi exited at 22:42:46 12.062u 0.476s 0:12.85 97.5% 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 Mon Oct 10 2011 at 22:42:46 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2274 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.066498 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): -0.2010000 52.04100 ymin,ymax (A): -19.75100 22.62100 zmin,zma (A): -8.708000 39.67900 x,y,z range (A): 52.24200 42.37200 48.38700 scale (grids/A): 3.066498 object centre (A): 25.92000 1.435000 15.48550 number of atom coordinates read : 2274 total number of charged atoms : 2146 net assigned charge : 1.000010 assigned positive charge : 340.6741 centred at (gu) : 92.32651 89.06081 90.05811 assigned negative charge : -339.6748 centred at (gu) : 93.25893 88.38197 91.41993 start vw surface at 0.1000000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 179434 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20271 grid for indexing accessible points = 1.400000 m= 93225 mr = 130434 m= 36410 mr = 77239 m= 10177 mr = 29799 m= 1964 mr = 7922 m= 197 mr = 1401 m= 2 mr = 99 m= 0 mr = 0 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 2170 time to turn everything in is 1.720000 number of dielectric boundary points 74515 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.860000 number of grid points assigned charge 17168 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) : 2.044332 object centre at (A) : 25.92000 1.435000 15.48550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6229799 -0.5997138 midg,1,midg; midg,igrid,midg -0.1538234 0.2211019 1,midg,midg; igrid,midg,midg -0.1827555 -0.6138093 gauss-seidel spectral radius is 0.9992881 estimated iterations to convergence 296 setup time was (sec) 2.080000 now iterating at: 22:42:48 rms-change max change #iterations 10.22880 515.4274 at 10iterations 6.000590 127.8752 at 20iterations 3.505594 65.75119 at 30iterations 2.050167 41.11092 at 40iterations 1.191621 20.81415 at 50iterations 0.6936035 12.27435 at 60iterations 0.4026027 6.998277 at 70iterations 0.2338404 4.092065 at 80iterations 0.1361347 2.467752 at 90iterations 7.8773081E-02 1.367981 at 100iterations 4.5831501E-02 0.8112884 at 110iterations 2.6563926E-02 0.4934492 at 120iterations 1.5404068E-02 0.2554340 at 130iterations 8.9391237E-03 0.1435471 at 140iterations 5.1914989E-03 8.5658073E-02 at 150iterations 3.0080522E-03 4.9608231E-02 at 160iterations 1.7478327E-03 3.0929565E-02 at 170iterations 1.0135691E-03 1.8836021E-02 at 180iterations finished qdiffx linear iterations at : 22:43:07 total time elapsed so far: 20.77000 # loops : 180 mean,max change (kT/e) : 1.0135691E-03 1.8836021E-02 energy calculations done at 20.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.93000 DelPhi exited at 22:43:08 20.935u 0.554s 0:21.79 98.5% 0+0k 0+0io 0pf+0w