Tue Oct 11 03:21:26 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 Tue Oct 11 2011 at 03:21:26 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: 242 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3130 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5608507 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): -24.05900 33.26000 ymin,ymax (A): -38.61500 22.52400 zmin,zma (A): -31.50200 31.97300 x,y,z range (A): 57.31900 61.13900 63.47500 scale (grids/A): 0.5608507 object centre (A): 4.600501 -8.045499 0.2355003 number of atom coordinates read : 3130 total number of charged atoms : 2975 net assigned charge : -3.999982 assigned positive charge : 464.5051 centred at (gu) : 90.29465 91.35592 91.87376 assigned negative charge : -468.5064 centred at (gu) : 90.35112 91.23452 91.87926 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6649 nv = 96 ne = 84 npr = 60175 no. pairs analyzed = 60175 no. exposed pairs = 4437 no. arc points = 31608 no. surface atoms = 1479 nbur = 1651 mkacc time = 0.1100000 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 = 1.540000 m= 274 mr = 3185 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3734 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3116 ## 396 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8481 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5222124E-10 -8.1231966E-10 midg,1,midg; midg,igrid,midg -1.3900052E-09 1.3764720E-09 1,midg,midg; igrid,midg,midg 2.0054999E-10 -1.2177159E-09 gauss-seidel spectral radius is 0.9836270 estimated iterations to convergence 64 setup time was (sec) 0.4100000 now iterating at: 03:21:27 rms-change max change #iterations 8.3589733E-02 14.47665 at 10iterations 5.9564929E-03 0.9236069 at 20iterations 4.2352953E-04 6.8140984E-02 at 30iterations 3.1501891E-05 5.0830841E-03 at 40iterations 2.5085287E-06 4.2343140E-04 at 50iterations finished qdiffx linear iterations at : 03:21:30 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 2.5085287E-06 4.2343140E-04 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 03:21:30 3.445u 0.173s 0:04.04 89.3% 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 Tue Oct 11 2011 at 03:21:30 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: 242 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3130 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: 1.682552 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): -24.05900 33.26000 ymin,ymax (A): -38.61500 22.52400 zmin,zma (A): -31.50200 31.97300 x,y,z range (A): 57.31900 61.13900 63.47500 scale (grids/A): 1.682552 object centre (A): 4.600501 -8.045499 0.2355003 number of atom coordinates read : 3130 total number of charged atoms : 2975 net assigned charge : -3.999982 assigned positive charge : 464.5051 centred at (gu) : 90.88313 94.06721 95.62036 assigned negative charge : -468.5064 centred at (gu) : 91.05337 93.70322 95.63746 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 72115 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31608 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 22341 mr = 46456 m= 2295 mr = 14740 m= 85 mr = 1024 m= 0 mr = 9 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 34607 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 302 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 22946 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) : 0.5608507 object centre at (A) : 4.600501 -8.045499 0.2355003 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6823752E-02 -9.0775471E-03 midg,1,midg; midg,igrid,midg -2.1629782E-02 -1.2133352E-02 1,midg,midg; igrid,midg,midg 9.0528894E-03 -8.7096905E-03 gauss-seidel spectral radius is 0.9983277 estimated iterations to convergence 194 setup time was (sec) 0.5800000 now iterating at: 03:21:31 rms-change max change #iterations 3.637063 157.5891 at 10iterations 1.561430 54.97511 at 20iterations 0.6722938 24.05979 at 30iterations 0.2903168 11.17153 at 40iterations 0.1242581 4.354768 at 50iterations 5.3501595E-02 2.053757 at 60iterations 2.3069771E-02 0.7665982 at 70iterations 9.9860020E-03 0.3881721 at 80iterations 4.2906078E-03 0.1374173 at 90iterations 1.8526779E-03 6.0463905E-02 at 100iterations 8.0183463E-04 2.8594971E-02 at 110iterations 3.4427553E-04 1.2161255E-02 at 120iterations finished qdiffx linear iterations at : 03:21:38 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 3.4427553E-04 1.2161255E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 03:21:39 7.858u 0.191s 0:08.34 96.4% 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 03:21:39 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: 242 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3130 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.523828 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): -24.05900 33.26000 ymin,ymax (A): -38.61500 22.52400 zmin,zma (A): -31.50200 31.97300 x,y,z range (A): 57.31900 61.13900 63.47500 scale (grids/A): 2.523828 object centre (A): 4.600501 -8.045499 0.2355003 number of atom coordinates read : 3130 total number of charged atoms : 2975 net assigned charge : -3.999982 assigned positive charge : 464.5051 centred at (gu) : 91.32452 96.10073 98.43049 assigned negative charge : -468.5064 centred at (gu) : 91.57994 95.55473 98.45613 start vw surface at 0.1000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 167041 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31608 grid for indexing accessible points = 1.400000 m= 75715 mr = 113847 m= 22260 mr = 58328 m= 3619 mr = 16255 m= 308 mr = 2204 m= 9 mr = 138 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8700000 number of dielectric boundary points 78180 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 23783 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) : 1.682552 object centre at (A) : 4.600501 -8.045499 0.2355003 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2746634 -9.8987229E-02 midg,1,midg; midg,igrid,midg -0.3850098 -0.2893467 1,midg,midg; igrid,midg,midg 0.1011886 -0.1090271 gauss-seidel spectral radius is 0.9992006 estimated iterations to convergence 279 setup time was (sec) 1.120000 now iterating at: 03:21:40 rms-change max change #iterations 9.503898 408.8901 at 10iterations 5.502421 160.3304 at 20iterations 3.170760 92.13826 at 30iterations 1.812615 43.86810 at 40iterations 1.031444 19.76236 at 50iterations 0.5828062 15.19779 at 60iterations 0.3306769 7.033497 at 70iterations 0.1868141 3.844087 at 80iterations 0.1050711 2.118774 at 90iterations 5.9179801E-02 1.406128 at 100iterations 3.3302274E-02 0.6466856 at 110iterations 1.8761901E-02 0.3595891 at 120iterations 1.0519156E-02 0.1981068 at 130iterations 5.9243464E-03 0.1174459 at 140iterations 3.3337881E-03 6.4314842E-02 at 150iterations 1.8714392E-03 3.6879539E-02 at 160iterations 1.0498926E-03 1.9268036E-02 at 170iterations 5.8878644E-04 1.1738777E-02 at 180iterations finished qdiffx linear iterations at : 03:21:52 total time elapsed so far: 12.59000 # loops : 180 mean,max change (kT/e) : 5.8878644E-04 1.1738777E-02 energy calculations done at 12.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.72000 DelPhi exited at 03:21:52 12.725u 0.202s 0:13.29 97.2% 0+0k 0+0io 0pf+0w