Mon Oct 10 18:51:33 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 18:51:34 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2356 !!! WARNING: HIR 86 has a net charge of 0.5140 !!! WARNING: HIR 257 has a net charge of 0.5140 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: 0.6254721 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): 48.02500 101.4600 ymin,ymax (A): 12.28600 69.20300 zmin,zma (A): 20.52700 64.29500 x,y,z range (A): 53.43500 56.91700 43.76800 scale (grids/A): 0.6254721 object centre (A): 74.74250 40.74450 42.41100 number of atom coordinates read : 2356 total number of charged atoms : 2218 net assigned charge : 2.028005 assigned positive charge : 354.2379 centred at (gu) : 89.50441 88.22444 91.40009 assigned negative charge : -352.2106 centred at (gu) : 89.41603 88.23249 91.53577 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6259 nv = 96 ne = 84 npr = 47147 no. pairs analyzed = 47147 no. exposed pairs = 3011 no. arc points = 20536 no. surface atoms = 1019 nbur = 1337 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 365 mr = 3488 m= 2 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.2800000 number of dielectric boundary points 3101 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2009 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7514 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.4474259E-09 -1.0410675E-08 midg,1,midg; midg,igrid,midg 3.9119032E-09 1.0638497E-09 1,midg,midg; igrid,midg,midg -4.6637232E-09 7.3898292E-09 gauss-seidel spectral radius is 0.9867420 estimated iterations to convergence 71 setup time was (sec) 0.5300000 now iterating at: 18:51:34 rms-change max change #iterations 0.1235403 17.11939 at 10iterations 1.1956687E-02 1.694284 at 20iterations 1.3119201E-03 0.2109795 at 30iterations 2.2376912E-04 3.9273262E-02 at 40iterations 5.4435579E-05 9.9892616E-03 at 50iterations finished qdiffx linear iterations at : 18:51:37 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 5.4435579E-05 9.9892616E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 18:51:38 3.493u 0.208s 0:04.01 92.0% 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 18:51:38 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2356 !!! WARNING: HIR 86 has a net charge of 0.5140 !!! WARNING: HIR 257 has a net charge of 0.5140 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: 1.876416 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): 48.02500 101.4600 ymin,ymax (A): 12.28600 69.20300 zmin,zma (A): 20.52700 64.29500 x,y,z range (A): 53.43500 56.91700 43.76800 scale (grids/A): 1.876416 object centre (A): 74.74250 40.74450 42.41100 number of atom coordinates read : 2356 total number of charged atoms : 2218 net assigned charge : 2.028005 assigned positive charge : 354.2379 centred at (gu) : 88.51292 84.67280 94.19953 assigned negative charge : -352.2106 centred at (gu) : 88.24793 84.69726 94.60716 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 67839 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20536 grid for indexing accessible points = 1.400000 m= 25770 mr = 47568 m= 4310 mr = 19168 m= 212 mr = 2730 m= 3 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 456 time to turn everything in is 0.5500000 number of dielectric boundary points 28626 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 103 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 17399 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) : 0.6254721 object centre at (A) : 74.74250 40.74450 42.41100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5221648E-02 -7.8273090E-03 midg,1,midg; midg,igrid,midg -1.6784189E-02 2.1184513E-02 1,midg,midg; igrid,midg,midg -1.4125298E-02 3.5271797E-02 gauss-seidel spectral radius is 0.9985717 estimated iterations to convergence 210 setup time was (sec) 0.8500000 now iterating at: 18:51:39 rms-change max change #iterations 3.914507 185.8195 at 10iterations 1.795845 69.15305 at 20iterations 0.8293834 28.54831 at 30iterations 0.3826266 15.00883 at 40iterations 0.1757127 5.903999 at 50iterations 8.0888838E-02 2.680145 at 60iterations 3.7393250E-02 1.319799 at 70iterations 1.7229838E-02 0.6249275 at 80iterations 8.0149220E-03 0.2573948 at 90iterations 3.7341753E-03 0.1219482 at 100iterations 1.7671935E-03 5.8483124E-02 at 110iterations 8.5734460E-04 2.7109146E-02 at 120iterations finished qdiffx linear iterations at : 18:51:45 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 8.5734460E-04 2.7109146E-02 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 18:51:46 7.938u 0.210s 0:08.54 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 Mon Oct 10 2011 at 18:51:46 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2356 !!! WARNING: HIR 86 has a net charge of 0.5140 !!! WARNING: HIR 257 has a net charge of 0.5140 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: 2.814625 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): 48.02500 101.4600 ymin,ymax (A): 12.28600 69.20300 zmin,zma (A): 20.52700 64.29500 x,y,z range (A): 53.43500 56.91700 43.76800 scale (grids/A): 2.814625 object centre (A): 74.74250 40.74450 42.41100 number of atom coordinates read : 2356 total number of charged atoms : 2218 net assigned charge : 2.028005 assigned positive charge : 354.2379 centred at (gu) : 87.76914 82.00899 96.29921 assigned negative charge : -352.2106 centred at (gu) : 87.37193 82.04578 96.91069 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 156864 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20536 grid for indexing accessible points = 1.400000 m= 81531 mr = 115398 m= 31638 mr = 67017 m= 7915 mr = 25625 m= 1012 mr = 5937 m= 40 mr = 616 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 1663 time to turn everything in is 1.370000 number of dielectric boundary points 64405 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 17742 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) : 1.876416 object centre at (A) : 74.74250 40.74450 42.41100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1629420 -4.2342607E-02 midg,1,midg; midg,igrid,midg -0.2901479 0.5016894 1,midg,midg; igrid,midg,midg -0.2387845 0.5985001 gauss-seidel spectral radius is 0.9992378 estimated iterations to convergence 286 setup time was (sec) 1.710000 now iterating at: 18:51:48 rms-change max change #iterations 9.375289 355.2593 at 10iterations 5.490000 140.9642 at 20iterations 3.182946 75.18835 at 30iterations 1.838446 41.87914 at 40iterations 1.056195 21.51655 at 50iterations 0.6063290 12.63745 at 60iterations 0.3479747 7.220068 at 70iterations 0.1991226 3.862587 at 80iterations 0.1137754 2.495005 at 90iterations 6.5252177E-02 1.271564 at 100iterations 3.7272654E-02 0.7651196 at 110iterations 2.1298829E-02 0.3917656 at 120iterations 1.2144677E-02 0.2452288 at 130iterations 6.9522932E-03 0.1366577 at 140iterations 3.9818119E-03 7.0922852E-02 at 150iterations 2.2937236E-03 4.8503876E-02 at 160iterations 1.3356302E-03 2.6553154E-02 at 170iterations 7.8977249E-04 1.5580237E-02 at 180iterations finished qdiffx linear iterations at : 18:51:59 total time elapsed so far: 12.60000 # loops : 180 mean,max change (kT/e) : 7.8977249E-04 1.5580237E-02 energy calculations done at 12.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.80000 DelPhi exited at 18:52:01 12.801u 0.202s 0:14.61 88.9% 0+0k 0+0io 0pf+0w