Tue Oct 11 03:16:47 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 Tue Oct 11 2011 at 03:16:47 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3437 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5314940 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): -87.75000 -36.03600 ymin,ymax (A): -27.45900 29.54500 zmin,zma (A): 9.525001 76.50600 x,y,z range (A): 51.71400 57.00400 66.98100 scale (grids/A): 0.5314940 object centre (A): -61.89300 1.043000 43.01550 number of atom coordinates read : 3437 total number of charged atoms : 3289 net assigned charge : -12.49998 assigned positive charge : 514.5620 centred at (gu) : 89.35007 89.45095 89.01140 assigned negative charge : -527.0631 centred at (gu) : 89.16473 89.49224 89.06956 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 6253 nv = 96 ne = 84 npr = 68485 no. pairs analyzed = 68485 no. exposed pairs = 4647 no. arc points = 32446 no. surface atoms = 1552 nbur = 1885 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 = 1.596000 m= 236 mr = 3038 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 3444 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3193 ## 425 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 8275 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1436329E-10 -5.4353350E-10 midg,1,midg; midg,igrid,midg -2.8036190E-10 -5.3934435E-10 1,midg,midg; igrid,midg,midg -1.5196313E-09 3.2300274E-10 gauss-seidel spectral radius is 0.9817992 estimated iterations to convergence 61 setup time was (sec) 0.6700000 now iterating at: 03:16:48 rms-change max change #iterations 7.2958283E-02 12.01400 at 10iterations 4.5997258E-03 0.8884053 at 20iterations 4.5402220E-04 8.7192535E-02 at 30iterations 1.0969105E-04 2.4829865E-02 at 40iterations 3.3586224E-05 7.7819824E-03 at 50iterations finished qdiffx linear iterations at : 03:16:51 total time elapsed so far: 3.530000 # loops : 50 mean,max change (kT/e) : 3.3586224E-05 7.7819824E-03 energy calculations done at 3.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.730000 DelPhi exited at 03:16:52 3.736u 0.201s 0:04.28 91.8% 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 03:16:52 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3437 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.594482 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): -87.75000 -36.03600 ymin,ymax (A): -27.45900 29.54500 zmin,zma (A): 9.525001 76.50600 x,y,z range (A): 51.71400 57.00400 66.98100 scale (grids/A): 1.594482 object centre (A): -61.89300 1.043000 43.01550 number of atom coordinates read : 3437 total number of charged atoms : 3289 net assigned charge : -12.49998 assigned positive charge : 514.5620 centred at (gu) : 88.04925 88.35188 87.03333 assigned negative charge : -527.0631 centred at (gu) : 87.49352 88.47611 87.20834 start vw surface at 0.2100000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 68574 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32446 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 21365 mr = 44778 m= 2186 mr = 14373 m= 61 mr = 999 m= 0 mr = 8 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 87 time to turn everything in is 0.5700000 number of dielectric boundary points 32028 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 377 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 25014 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) : 0.5314940 object centre at (A) : -61.89300 1.043000 43.01550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.8840869E-03 -1.6062628E-02 midg,1,midg; midg,igrid,midg -6.6831266E-03 -2.9855839E-03 1,midg,midg; igrid,midg,midg -2.2686649E-02 3.7186802E-03 gauss-seidel spectral radius is 0.9981474 estimated iterations to convergence 185 setup time was (sec) 0.8500000 now iterating at: 03:16:53 rms-change max change #iterations 3.467702 157.7928 at 10iterations 1.426735 52.38234 at 20iterations 0.5886571 22.96191 at 30iterations 0.2432133 10.21507 at 40iterations 0.1005825 3.634433 at 50iterations 4.1575115E-02 1.538790 at 60iterations 1.7270958E-02 0.6103592 at 70iterations 7.1702315E-03 0.2367700 at 80iterations 3.0214577E-03 0.1115150 at 90iterations 1.3069304E-03 5.0243378E-02 at 100iterations 5.9871637E-04 2.4093628E-02 at 110iterations 3.0270321E-04 1.3872147E-02 at 120iterations finished qdiffx linear iterations at : 03:16:59 total time elapsed so far: 7.260000 # loops : 120 mean,max change (kT/e) : 3.0270321E-04 1.3872147E-02 energy calculations done at 7.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.450000 DelPhi exited at 03:16:59 7.453u 0.177s 0:07.92 96.2% 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 Tue Oct 11 2011 at 03:17:00 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3437 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.391723 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): -87.75000 -36.03600 ymin,ymax (A): -27.45900 29.54500 zmin,zma (A): 9.525001 76.50600 x,y,z range (A): 51.71400 57.00400 66.98100 scale (grids/A): 2.391723 object centre (A): -61.89300 1.043000 43.01550 number of atom coordinates read : 3437 total number of charged atoms : 3289 net assigned charge : -12.49998 assigned positive charge : 514.5620 centred at (gu) : 87.07363 87.52734 85.54973 assigned negative charge : -527.0631 centred at (gu) : 86.24020 87.71402 85.81232 start vw surface at 0.2600000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 158863 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32446 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 72809 mr = 109723 m= 21240 mr = 56597 m= 3293 mr = 15790 m= 194 mr = 2075 m= 8 mr = 56 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 333 time to turn everything in is 1.340000 number of dielectric boundary points 72167 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 26273 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) : 1.594482 object centre at (A) : -61.89300 1.043000 43.01550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1635701 -0.2650810 midg,1,midg; midg,igrid,midg -0.1683590 -1.5754117E-02 1,midg,midg; igrid,midg,midg -0.3600925 6.5234095E-02 gauss-seidel spectral radius is 0.9991413 estimated iterations to convergence 270 setup time was (sec) 1.640000 now iterating at: 03:17:01 rms-change max change #iterations 9.140740 311.2906 at 10iterations 5.135336 138.5271 at 20iterations 2.866504 75.73594 at 30iterations 1.596346 35.48145 at 40iterations 0.8840102 19.61635 at 50iterations 0.4896731 10.79498 at 60iterations 0.2704711 7.246149 at 70iterations 0.1500263 2.883923 at 80iterations 8.2670808E-02 1.694391 at 90iterations 4.5498930E-02 1.062592 at 100iterations 2.5008650E-02 0.4523158 at 110iterations 1.3777497E-02 0.2687101 at 120iterations 7.5905328E-03 0.1497965 at 130iterations 4.1853213E-03 8.2605362E-02 at 140iterations 2.3118281E-03 5.0931931E-02 at 150iterations 1.2745073E-03 2.5039673E-02 at 160iterations 7.0728728E-04 1.5730143E-02 at 170iterations 3.9786904E-04 8.7718964E-03 at 180iterations finished qdiffx linear iterations at : 03:17:12 total time elapsed so far: 11.80000 # loops : 180 mean,max change (kT/e) : 3.9786904E-04 8.7718964E-03 energy calculations done at 11.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.01000 DelPhi exited at 03:17:12 12.012u 0.181s 0:12.72 95.8% 0+0k 0+0io 0pf+0w