Sat Oct 15 12:06:40 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 Sat Oct 15 2011 at 12:06:40 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3255 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5929973 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): -16.73300 40.24000 ymin,ymax (A): 16.54700 76.58100 zmin,zma (A): 25.28500 83.34800 x,y,z range (A): 56.97300 60.03400 58.06300 scale (grids/A): 0.5929973 object centre (A): 11.75350 46.56400 54.31650 number of atom coordinates read : 3255 total number of charged atoms : 3113 net assigned charge : 10.95703 assigned positive charge : 480.2957 centred at (gu) : 90.25538 90.22837 91.94152 assigned negative charge : -469.3404 centred at (gu) : 90.13427 90.26230 92.14404 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7977 nv = 96 ne = 84 npr = 62914 no. pairs analyzed = 62914 no. exposed pairs = 4305 no. arc points = 31628 no. surface atoms = 1427 nbur = 1828 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 371 mr = 4102 m= 3 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 4214 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3139 ## 333 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9809 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.9791661E-09 -5.5897682E-09 midg,1,midg; midg,igrid,midg 4.8067328E-09 2.8042342E-09 1,midg,midg; igrid,midg,midg -4.2332463E-10 8.5630614E-09 gauss-seidel spectral radius is 0.9853562 estimated iterations to convergence 68 setup time was (sec) 0.6200000 now iterating at: 12:06:41 rms-change max change #iterations 0.1143327 15.80135 at 10iterations 9.3624787E-03 1.740005 at 20iterations 7.9267798E-04 0.1254710 at 30iterations 7.5549993E-05 9.4604492E-03 at 40iterations 9.8616865E-06 9.8609924E-04 at 50iterations finished qdiffx linear iterations at : 12:06:44 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 9.8616865E-06 9.8609924E-04 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 12:06:44 3.559u 0.163s 0:04.06 91.3% 0+0k 0+0io 6pf+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 Sat Oct 15 2011 at 12:06:44 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3255 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.778992 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): -16.73300 40.24000 ymin,ymax (A): 16.54700 76.58100 zmin,zma (A): 25.28500 83.34800 x,y,z range (A): 56.97300 60.03400 58.06300 scale (grids/A): 1.778992 object centre (A): 11.75350 46.56400 54.31650 number of atom coordinates read : 3255 total number of charged atoms : 3113 net assigned charge : 10.95703 assigned positive charge : 480.2957 centred at (gu) : 90.76552 90.68420 95.82375 assigned negative charge : -469.3404 centred at (gu) : 90.40268 90.78652 96.43187 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 86749 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31628 grid for indexing accessible points = 1.400000 m= 28982 mr = 58400 m= 3784 mr = 20315 m= 162 mr = 2055 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 463 time to turn everything in is 0.6100000 number of dielectric boundary points 38880 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 277 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 24268 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) : 0.5929973 object centre at (A) : 11.75350 46.56400 54.31650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3131121E-02 1.8071110E-03 midg,1,midg; midg,igrid,midg 4.1899104E-02 2.0544607E-02 1,midg,midg; igrid,midg,midg -9.2767198E-03 1.6645903E-02 gauss-seidel spectral radius is 0.9985245 estimated iterations to convergence 206 setup time was (sec) 0.9300000 now iterating at: 12:06:45 rms-change max change #iterations 4.157389 215.5021 at 10iterations 1.878242 64.00307 at 20iterations 0.8526262 30.27575 at 30iterations 0.3849467 11.48481 at 40iterations 0.1750375 5.631529 at 50iterations 7.9241879E-02 2.362576 at 60iterations 3.5949983E-02 1.155178 at 70iterations 1.6345445E-02 0.4673042 at 80iterations 7.3849084E-03 0.2313781 at 90iterations 3.3680617E-03 0.1060524 at 100iterations 1.5293886E-03 5.4787636E-02 at 110iterations 6.9645100E-04 2.1131516E-02 at 120iterations finished qdiffx linear iterations at : 12:06:52 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 6.9645100E-04 2.1131516E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.020000 DelPhi exited at 12:06:53 8.025u 0.244s 0:08.66 95.3% 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 Sat Oct 15 2011 at 12:06:53 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3255 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 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: 2.668488 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): -16.73300 40.24000 ymin,ymax (A): 16.54700 76.58100 zmin,zma (A): 25.28500 83.34800 x,y,z range (A): 56.97300 60.03400 58.06300 scale (grids/A): 2.668488 object centre (A): 11.75350 46.56400 54.31650 number of atom coordinates read : 3255 total number of charged atoms : 3113 net assigned charge : 10.95703 assigned positive charge : 480.2957 centred at (gu) : 91.14813 91.02599 98.73578 assigned negative charge : -469.3404 centred at (gu) : 90.60403 91.17982 99.64778 start vw surface at 0.1600000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 200933 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31628 grid for indexing accessible points = 1.400000 m= 96442 mr = 142599 m= 31279 mr = 76526 m= 6372 mr = 23978 m= 653 mr = 4387 m= 15 mr = 349 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 1558 time to turn everything in is 1.600000 number of dielectric boundary points 87855 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 24892 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) : 1.778992 object centre at (A) : 11.75350 46.56400 54.31650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6230310 1.3469173E-02 midg,1,midg; midg,igrid,midg 0.5935293 0.4625960 1,midg,midg; igrid,midg,midg -6.2196996E-02 0.1996718 gauss-seidel spectral radius is 0.9992594 estimated iterations to convergence 290 setup time was (sec) 1.940000 now iterating at: 12:06:55 rms-change max change #iterations 10.27321 324.7165 at 10iterations 6.056886 150.7141 at 20iterations 3.549932 78.34534 at 30iterations 2.063063 48.06601 at 40iterations 1.201206 25.01046 at 50iterations 0.6964033 16.22139 at 60iterations 0.4016304 7.396011 at 70iterations 0.2318477 4.284210 at 80iterations 0.1337276 2.831501 at 90iterations 7.7044457E-02 1.428074 at 100iterations 4.4252653E-02 0.7909842 at 110iterations 2.5500922E-02 0.4580059 at 120iterations 1.4653029E-02 0.2880220 at 130iterations 8.4132906E-03 0.1459465 at 140iterations 4.8440793E-03 8.1073761E-02 at 150iterations 2.7823916E-03 5.1959991E-02 at 160iterations 1.5971641E-03 2.7595520E-02 at 170iterations 9.1715582E-04 1.6541481E-02 at 180iterations finished qdiffx linear iterations at : 12:07:06 total time elapsed so far: 13.02000 # loops : 180 mean,max change (kT/e) : 9.1715582E-04 1.6541481E-02 energy calculations done at 13.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.20000 DelPhi exited at 12:07:07 13.205u 0.248s 0:13.81 97.3% 0+0k 0+0io 0pf+0w