Mon Oct 10 13:59:40 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+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 13:59:40 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3214 !!! WARNING: GLM 72 has a net charge of -0.0940 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: 0.5228451 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): -8.243000 59.84600 ymin,ymax (A): -14.24900 34.12200 zmin,zma (A): 18.76400 70.66700 x,y,z range (A): 68.08900 48.37100 51.90300 scale (grids/A): 0.5228451 object centre (A): 25.80150 9.936501 44.71550 number of atom coordinates read : 3214 total number of charged atoms : 3063 net assigned charge : 7.906035 assigned positive charge : 492.6479 centred at (gu) : 90.79619 90.56871 89.30773 assigned negative charge : -484.7431 centred at (gu) : 90.81673 90.61591 89.23460 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 5602 nv = 96 ne = 84 npr = 64053 no. pairs analyzed = 64053 no. exposed pairs = 4063 no. arc points = 28156 no. surface atoms = 1360 nbur = 1854 mkacc time = 0.1800000 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 = 1.652000 m= 235 mr = 2870 m= 0 mr = 6 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 2961 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2783 ## 388 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 7424 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8474152E-11 3.4086137E-10 midg,1,midg; midg,igrid,midg 2.8722086E-10 6.2484698E-11 1,midg,midg; igrid,midg,midg 2.0819654E-10 1.6297551E-10 gauss-seidel spectral radius is 0.9811730 estimated iterations to convergence 60 setup time was (sec) 0.6600000 now iterating at: 13:59:41 rms-change max change #iterations 6.1759010E-02 12.85375 at 10iterations 3.8417827E-03 0.6655464 at 20iterations 4.8521816E-04 7.6408386E-02 at 30iterations 1.8260199E-04 2.7019501E-02 at 40iterations 8.6200700E-05 1.3359785E-02 at 50iterations finished qdiffx linear iterations at : 13:59:44 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 8.6200700E-05 1.3359785E-02 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.130000 DelPhi exited at 13:59:45 4.137u 0.262s 0:05.09 86.2% 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 Mon Oct 10 2011 at 13:59:45 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3214 !!! WARNING: GLM 72 has a net charge of -0.0940 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: 1.568535 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): -8.243000 59.84600 ymin,ymax (A): -14.24900 34.12200 zmin,zma (A): 18.76400 70.66700 x,y,z range (A): 68.08900 48.37100 51.90300 scale (grids/A): 1.568535 object centre (A): 25.80150 9.936501 44.71550 number of atom coordinates read : 3214 total number of charged atoms : 3063 net assigned charge : 7.906035 assigned positive charge : 492.6479 centred at (gu) : 92.38773 91.70522 87.92271 assigned negative charge : -484.7431 centred at (gu) : 92.44965 91.84744 87.70344 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 62971 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28156 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 19529 mr = 42892 m= 1967 mr = 13146 m= 47 mr = 823 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 149 time to turn everything in is 0.5900000 number of dielectric boundary points 27653 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 373 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 23161 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) : 0.5228451 object centre at (A) : 25.80150 9.936501 44.71550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8393828E-03 5.6529166E-03 midg,1,midg; midg,igrid,midg 6.0502691E-03 -2.5732897E-03 1,midg,midg; igrid,midg,midg 1.5261978E-02 6.1707739E-03 gauss-seidel spectral radius is 0.9980428 estimated iterations to convergence 180 setup time was (sec) 0.8800000 now iterating at: 13:59:46 rms-change max change #iterations 3.197945 187.9227 at 10iterations 1.294689 51.57499 at 20iterations 0.5202982 19.58312 at 30iterations 0.2110267 8.071978 at 40iterations 8.5258223E-02 3.100222 at 50iterations 3.4578156E-02 1.190804 at 60iterations 1.4021069E-02 0.4866486 at 70iterations 5.6925993E-03 0.1999207 at 80iterations 2.3726376E-03 8.7432861E-02 at 90iterations 1.0323481E-03 3.8925171E-02 at 100iterations 5.1000062E-04 2.0300865E-02 at 110iterations 3.0698656E-04 1.0635853E-02 at 120iterations finished qdiffx linear iterations at : 13:59:55 total time elapsed so far: 9.010000 # loops : 120 mean,max change (kT/e) : 3.0698656E-04 1.0635853E-02 energy calculations done at 9.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.190000 DelPhi exited at 13:59:56 9.190u 0.292s 0:10.42 90.9% 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 13:59:56 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3214 !!! WARNING: GLM 72 has a net charge of -0.0940 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: 2.352803 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): -8.243000 59.84600 ymin,ymax (A): -14.24900 34.12200 zmin,zma (A): 18.76400 70.66700 x,y,z range (A): 68.08900 48.37100 51.90300 scale (grids/A): 2.352803 object centre (A): 25.80150 9.936501 44.71550 number of atom coordinates read : 3214 total number of charged atoms : 3063 net assigned charge : 7.906035 assigned positive charge : 492.6479 centred at (gu) : 93.58145 92.55756 86.88381 assigned negative charge : -484.7431 centred at (gu) : 93.67439 92.77102 86.55498 start vw surface at 0.1800000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 146503 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28156 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 67646 mr = 105758 m= 19091 mr = 52500 m= 2825 mr = 13920 m= 171 mr = 1628 m= 0 mr = 81 time to grow re-entrant surface = 0.8699999 no. cavity mid-points inaccessible to solvent = 552 time to turn everything in is 1.430000 number of dielectric boundary points 62349 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 24459 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) : 1.568535 object centre at (A) : 25.80150 9.936501 44.71550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1879023E-02 7.6744184E-02 midg,1,midg; midg,igrid,midg 0.1206377 -7.4863888E-02 1,midg,midg; igrid,midg,midg 0.6187832 -1.6753448E-02 gauss-seidel spectral radius is 0.9990976 estimated iterations to convergence 263 setup time was (sec) 1.740000 now iterating at: 13:59:58 rms-change max change #iterations 8.567073 232.9029 at 10iterations 4.786712 143.6635 at 20iterations 2.662217 72.13351 at 30iterations 1.470757 34.23338 at 40iterations 0.8073713 18.56661 at 50iterations 0.4433482 10.68007 at 60iterations 0.2425208 5.888626 at 70iterations 0.1328391 3.351451 at 80iterations 7.2594441E-02 1.730910 at 90iterations 3.9548676E-02 0.8381462 at 100iterations 2.1597281E-02 0.4673986 at 110iterations 1.1770511E-02 0.2478256 at 120iterations 6.3855592E-03 0.1388559 at 130iterations 3.4880883E-03 8.0746651E-02 at 140iterations 1.9006322E-03 4.1786194E-02 at 150iterations 1.0389109E-03 2.2285461E-02 at 160iterations 5.6429248E-04 1.2201309E-02 at 170iterations 3.0964901E-04 7.4081421E-03 at 180iterations finished qdiffx linear iterations at : 14:00:11 total time elapsed so far: 14.99000 # loops : 180 mean,max change (kT/e) : 3.0964901E-04 7.4081421E-03 energy calculations done at 14.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.16000 DelPhi exited at 14:00:12 15.161u 0.304s 0:15.90 97.2% 0+0k 0+0io 0pf+0w