Sun Oct 9 02:19:47 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 Sun Oct 9 2011 at 02:19:47 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2018 !!! WARNING: MG2 215 has a net charge of 1.4000 !!! WARNING: SAM 216 has a net charge of -0.6000 !!! WARNING: SAM 1 has a net charge of -0.5000 !!! WARNING: SAM 3 has a net charge of 0.3950 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: 0.7158081 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): -32.89800 16.83600 ymin,ymax (A): -29.95400 17.52400 zmin,zma (A): -36.07500 9.286000 x,y,z range (A): 49.73400 47.47800 45.36100 scale (grids/A): 0.7158081 object centre (A): -8.030999 -6.215000 -13.39450 number of atom coordinates read : 2018 total number of charged atoms : 1930 net assigned charge : -5.304990 assigned positive charge : 307.8018 centred at (gu) : 89.16341 89.85081 92.25909 assigned negative charge : -313.1070 centred at (gu) : 89.16526 89.86642 92.21571 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7300 nv = 96 ne = 84 npr = 40959 no. pairs analyzed = 40959 no. exposed pairs = 2285 no. arc points = 16109 no. surface atoms = 773 nbur = 1245 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 505 mr = 4485 m= 2 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 215 time to turn everything in is 0.3000000 number of dielectric boundary points 3206 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1350 ## 104 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7898 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.2838903E-08 -4.3559094E-08 midg,1,midg; midg,igrid,midg -4.6805209E-08 -6.2301353E-08 1,midg,midg; igrid,midg,midg -6.2765174E-08 -4.7864159E-08 gauss-seidel spectral radius is 0.9898213 estimated iterations to convergence 81 setup time was (sec) 0.5700000 now iterating at: 02:19:48 rms-change max change #iterations 0.2162393 30.75448 at 10iterations 2.7384307E-02 4.071823 at 20iterations 3.4696413E-03 0.4378242 at 30iterations 4.3544691E-04 5.0151348E-02 at 40iterations 5.4896747E-05 7.5435638E-03 at 50iterations finished qdiffx linear iterations at : 02:19:51 total time elapsed so far: 3.830000 # loops : 50 mean,max change (kT/e) : 5.4896747E-05 7.5435638E-03 energy calculations done at 3.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.000000 DelPhi exited at 02:19:51 4.006u 0.252s 0:04.56 93.2% 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 Sun Oct 9 2011 at 02:19:51 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2018 !!! WARNING: MG2 215 has a net charge of 1.4000 !!! WARNING: SAM 216 has a net charge of -0.6000 !!! WARNING: SAM 1 has a net charge of -0.5000 !!! WARNING: SAM 3 has a net charge of 0.3950 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: 2.147424 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): -32.89800 16.83600 ymin,ymax (A): -29.95400 17.52400 zmin,zma (A): -36.07500 9.286000 x,y,z range (A): 49.73400 47.47800 45.36100 scale (grids/A): 2.147424 object centre (A): -8.030999 -6.215000 -13.39450 number of atom coordinates read : 2018 total number of charged atoms : 1930 net assigned charge : -5.304990 assigned positive charge : 307.8018 centred at (gu) : 87.49017 89.55224 96.77728 assigned negative charge : -313.1070 centred at (gu) : 87.49580 89.59936 96.64729 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 77395 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16109 grid for indexing accessible points = 1.400000 m= 32318 mr = 56499 m= 6919 mr = 25915 m= 665 mr = 5058 m= 17 mr = 389 m= 0 mr = 2 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 5909 time to turn everything in is 0.7100000 number of dielectric boundary points 29451 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 40 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 15337 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) : 0.7158081 object centre at (A) : -8.030999 -6.215000 -13.39450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6064141E-02 -1.8046118E-02 midg,1,midg; midg,igrid,midg -4.2798534E-02 -2.0663816E-02 1,midg,midg; igrid,midg,midg -1.7542673E-02 -2.5587637E-02 gauss-seidel spectral radius is 0.9988461 estimated iterations to convergence 233 setup time was (sec) 1.010000 now iterating at: 02:19:53 rms-change max change #iterations 4.721729 204.9122 at 10iterations 2.351276 73.37353 at 20iterations 1.172104 38.80602 at 30iterations 0.5836930 17.14148 at 40iterations 0.2909954 8.877806 at 50iterations 0.1452069 4.230274 at 60iterations 7.2484657E-02 2.355181 at 70iterations 3.6027793E-02 1.079052 at 80iterations 1.8018827E-02 0.5253463 at 90iterations 8.9699319E-03 0.2599449 at 100iterations 4.4766772E-03 0.1183147 at 110iterations 2.2386955E-03 7.0916176E-02 at 120iterations finished qdiffx linear iterations at : 02:20:01 total time elapsed so far: 9.210000 # loops : 120 mean,max change (kT/e) : 2.2386955E-03 7.0916176E-02 energy calculations done at 9.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.390000 DelPhi exited at 02:20:01 9.394u 0.260s 0:09.93 97.1% 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 Sun Oct 9 2011 at 02:20:01 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2018 !!! WARNING: MG2 215 has a net charge of 1.4000 !!! WARNING: SAM 216 has a net charge of -0.6000 !!! WARNING: SAM 1 has a net charge of -0.5000 !!! WARNING: SAM 3 has a net charge of 0.3950 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: 3.221136 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): -32.89800 16.83600 ymin,ymax (A): -29.95400 17.52400 zmin,zma (A): -36.07500 9.286000 x,y,z range (A): 49.73400 47.47800 45.36100 scale (grids/A): 3.221136 object centre (A): -8.030999 -6.215000 -13.39450 number of atom coordinates read : 2018 total number of charged atoms : 1930 net assigned charge : -5.304990 assigned positive charge : 307.8018 centred at (gu) : 86.23527 89.32835 100.1659 assigned negative charge : -313.1070 centred at (gu) : 86.24379 89.39902 99.97097 start vw surface at 0.1400000 fill in re-entrant regions at 0.9900000 boundary points on vw surface= 178599 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16109 grid for indexing accessible points = 1.400000 m= 98769 mr = 135490 m= 43501 mr = 84763 m= 13481 mr = 37490 m= 2862 mr = 11128 m= 361 mr = 2169 m= 7 mr = 265 m= 0 mr = 3 time to grow re-entrant surface = 1.120000 no. cavity mid-points inaccessible to solvent = 19772 time to turn everything in is 2.240000 number of dielectric boundary points 66272 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.390000 number of grid points assigned charge 15440 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) : 2.147424 object centre at (A) : -8.030999 -6.215000 -13.39450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1167454 -0.2864575 midg,1,midg; midg,igrid,midg -0.5328215 -0.2199348 1,midg,midg; igrid,midg,midg 6.2827110E-02 -0.2435199 gauss-seidel spectral radius is 0.9992992 estimated iterations to convergence 298 setup time was (sec) 2.560000 now iterating at: 02:20:04 rms-change max change #iterations 10.33762 406.3748 at 10iterations 6.036592 121.5520 at 20iterations 3.527777 63.36423 at 30iterations 2.065827 36.26675 at 40iterations 1.203664 21.71143 at 50iterations 0.7027497 12.09620 at 60iterations 0.4110709 7.146669 at 70iterations 0.2391970 4.174973 at 80iterations 0.1396944 2.447350 at 90iterations 8.1500173E-02 1.393753 at 100iterations 4.7510535E-02 0.8323002 at 110iterations 2.7668849E-02 0.4559133 at 120iterations 1.6163329E-02 0.2648983 at 130iterations 9.4350642E-03 0.1560326 at 140iterations 5.4991040E-03 9.1218948E-02 at 150iterations 3.2019089E-03 5.4418564E-02 at 160iterations 1.8709364E-03 3.2583162E-02 at 170iterations 1.0936048E-03 1.8561363E-02 at 180iterations finished qdiffx linear iterations at : 02:20:19 total time elapsed so far: 17.57000 # loops : 180 mean,max change (kT/e) : 1.0936048E-03 1.8561363E-02 energy calculations done at 17.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.74000 DelPhi exited at 02:20:20 17.744u 0.301s 0:18.33 98.4% 0+0k 0+0io 0pf+0w