Sat Oct 15 14:28:57 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 14:28:57 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3184 !!! WARNING: GLN 355 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5985909 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): -24.54600 33.12400 ymin,ymax (A): -11.01300 43.58800 zmin,zma (A): 7.634000 67.10700 x,y,z range (A): 57.67000 54.60100 59.47300 scale (grids/A): 0.5985909 object centre (A): 4.289001 16.28750 37.37050 number of atom coordinates read : 3184 total number of charged atoms : 3041 net assigned charge : -5.271959 assigned positive charge : 478.5915 centred at (gu) : 89.97617 89.14150 91.05792 assigned negative charge : -483.8649 centred at (gu) : 90.05414 88.98490 91.16673 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7589 nv = 96 ne = 84 npr = 64242 no. pairs analyzed = 64242 no. exposed pairs = 4149 no. arc points = 28893 no. surface atoms = 1407 nbur = 1777 mkacc time = 0.1700000 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= 381 mr = 3981 m= 0 mr = 22 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.3600000 number of dielectric boundary points 3967 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2955 ## 276 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9560 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0531816E-09 -8.6833607E-09 midg,1,midg; midg,igrid,midg -1.0909434E-08 3.8058947E-09 1,midg,midg; igrid,midg,midg 1.3424165E-09 -5.4116578E-09 gauss-seidel spectral radius is 0.9856099 estimated iterations to convergence 68 setup time was (sec) 0.6100000 now iterating at: 14:28:58 rms-change max change #iterations 0.1162953 19.64480 at 10iterations 1.0023923E-02 1.434743 at 20iterations 8.2876190E-04 0.1194992 at 30iterations 7.0854992E-05 9.9754333E-03 at 40iterations 6.9663765E-06 1.1253357E-03 at 50iterations finished qdiffx linear iterations at : 14:29:04 total time elapsed so far: 3.910000 # loops : 50 mean,max change (kT/e) : 6.9663765E-06 1.1253357E-03 energy calculations done at 3.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 14:29:04 4.081u 0.435s 0:07.03 64.1% 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 Sat Oct 15 2011 at 14:29:04 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3184 !!! WARNING: GLN 355 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.795773 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): -24.54600 33.12400 ymin,ymax (A): -11.01300 43.58800 zmin,zma (A): 7.634000 67.10700 x,y,z range (A): 57.67000 54.60100 59.47300 scale (grids/A): 1.795773 object centre (A): 4.289001 16.28750 37.37050 number of atom coordinates read : 3184 total number of charged atoms : 3041 net assigned charge : -5.271959 assigned positive charge : 478.5915 centred at (gu) : 89.92757 87.42359 93.17292 assigned negative charge : -483.8649 centred at (gu) : 90.16190 86.95422 93.49988 start vw surface at 0.1300000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 83186 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28893 grid for indexing accessible points = 1.400000 m= 26963 mr = 56518 m= 3466 mr = 18585 m= 135 mr = 1785 m= 0 mr = 20 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1690 time to turn everything in is 0.6500000 number of dielectric boundary points 36842 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 225 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 23717 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) : 0.5985909 object centre at (A) : 4.289001 16.28750 37.37050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7901396E-02 8.1215287E-03 midg,1,midg; midg,igrid,midg -4.6063319E-02 4.5639356E-03 1,midg,midg; igrid,midg,midg 1.6849346E-02 -3.9746463E-02 gauss-seidel spectral radius is 0.9985306 estimated iterations to convergence 207 setup time was (sec) 1.010000 now iterating at: 14:29:07 rms-change max change #iterations 4.222029 174.6868 at 10iterations 1.909618 62.49805 at 20iterations 0.8617401 30.31333 at 30iterations 0.3934327 11.90422 at 40iterations 0.1784108 5.895106 at 50iterations 8.1106953E-02 2.539599 at 60iterations 3.6988862E-02 1.165387 at 70iterations 1.6760854E-02 0.5652313 at 80iterations 7.6152668E-03 0.2742558 at 90iterations 3.4707729E-03 0.1003723 at 100iterations 1.5814437E-03 4.8135757E-02 at 110iterations 7.2030246E-04 2.3465633E-02 at 120iterations finished qdiffx linear iterations at : 14:29:18 total time elapsed so far: 10.04000 # loops : 120 mean,max change (kT/e) : 7.2030246E-04 2.3465633E-02 energy calculations done at 10.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.22000 DelPhi exited at 14:29:19 10.228u 0.454s 0:14.65 72.8% 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 Sat Oct 15 2011 at 14:29:19 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3184 !!! WARNING: GLN 355 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.693659 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): -24.54600 33.12400 ymin,ymax (A): -11.01300 43.58800 zmin,zma (A): 7.634000 67.10700 x,y,z range (A): 57.67000 54.60100 59.47300 scale (grids/A): 2.693659 object centre (A): 4.289001 16.28750 37.37050 number of atom coordinates read : 3184 total number of charged atoms : 3041 net assigned charge : -5.271959 assigned positive charge : 478.5915 centred at (gu) : 89.89101 86.13517 94.75903 assigned negative charge : -483.8649 centred at (gu) : 90.24270 85.43111 95.24969 start vw surface at 0.1300000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 192834 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28893 grid for indexing accessible points = 1.400000 m= 91293 mr = 138085 m= 28793 mr = 72223 m= 5631 mr = 21723 m= 599 mr = 3721 m= 15 mr = 328 m= 0 mr = 0 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 5406 time to turn everything in is 1.680000 number of dielectric boundary points 83085 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 24322 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) : 1.795773 object centre at (A) : 4.289001 16.28750 37.37050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.0979459E-02 0.2665863 midg,1,midg; midg,igrid,midg -0.5524582 3.7103187E-02 1,midg,midg; igrid,midg,midg 0.3483819 -0.4580407 gauss-seidel spectral radius is 0.9992526 estimated iterations to convergence 289 setup time was (sec) 2.040000 now iterating at: 14:29:21 rms-change max change #iterations 10.41538 311.8207 at 10iterations 6.136613 153.1290 at 20iterations 3.578525 86.36566 at 30iterations 2.076175 41.88308 at 40iterations 1.203617 25.06882 at 50iterations 0.6944187 14.20147 at 60iterations 0.3998924 7.316339 at 70iterations 0.2304415 5.406327 at 80iterations 0.1325246 2.331765 at 90iterations 7.5932145E-02 1.744492 at 100iterations 4.3578014E-02 0.7567139 at 110iterations 2.5072793E-02 0.4406843 at 120iterations 1.4343151E-02 0.2439594 at 130iterations 8.2342057E-03 0.1594648 at 140iterations 4.7230152E-03 8.3236694E-02 at 150iterations 2.7055286E-03 4.7130585E-02 at 160iterations 1.5558711E-03 2.8812408E-02 at 170iterations 8.9246954E-04 1.5458584E-02 at 180iterations finished qdiffx linear iterations at : 14:29:45 total time elapsed so far: 18.11000 # loops : 180 mean,max change (kT/e) : 8.9246954E-04 1.5458584E-02 energy calculations done at 18.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.28000 DelPhi exited at 14:29:46 18.288u 0.476s 0:26.93 69.6% 0+0k 0+0io 0pf+0w