Tue Oct 11 03:19:20 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 Tue Oct 11 2011 at 03:19:21 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 = 3185 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: 0.5375126 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): -3.755000 46.19200 ymin,ymax (A): 70.83600 137.0670 zmin,zma (A): 102.6280 162.2500 x,y,z range (A): 49.94700 66.23100 59.62200 scale (grids/A): 0.5375126 object centre (A): 21.21850 103.9515 132.4390 number of atom coordinates read : 3185 total number of charged atoms : 3046 net assigned charge : -5.999976 assigned positive charge : 475.8608 centred at (gu) : 91.07348 92.94679 91.40680 assigned negative charge : -481.8619 centred at (gu) : 91.03323 92.97639 91.40434 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5740 nv = 96 ne = 84 npr = 66439 no. pairs analyzed = 66439 no. exposed pairs = 3857 no. arc points = 27002 no. surface atoms = 1301 nbur = 1884 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 = 1.596000 m= 248 mr = 3035 m= 0 mr = 6 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 2947 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2719 ## 374 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7736 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9424753E-10 -3.4969633E-10 midg,1,midg; midg,igrid,midg -5.6245012E-11 -8.6911028E-10 1,midg,midg; igrid,midg,midg -3.5920139E-10 -6.7583973E-11 gauss-seidel spectral radius is 0.9821703 estimated iterations to convergence 62 setup time was (sec) 0.4200000 now iterating at: 03:19:21 rms-change max change #iterations 7.1857676E-02 10.93704 at 10iterations 4.6545626E-03 0.8118725 at 20iterations 3.6738027E-04 6.4300537E-02 at 30iterations 4.9833136E-05 9.1879368E-03 at 40iterations 9.9958161E-06 2.0108353E-03 at 50iterations finished qdiffx linear iterations at : 03:19:24 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 9.9958161E-06 2.0108353E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 03:19:24 3.459u 0.167s 0:03.94 91.6% 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 03:19:25 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 = 3185 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: 1.612538 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): -3.755000 46.19200 ymin,ymax (A): 70.83600 137.0670 zmin,zma (A): 102.6280 162.2500 x,y,z range (A): 49.94700 66.23100 59.62200 scale (grids/A): 1.612538 object centre (A): 21.21850 103.9515 132.4390 number of atom coordinates read : 3185 total number of charged atoms : 3046 net assigned charge : -5.999976 assigned positive charge : 475.8608 centred at (gu) : 93.21954 98.83968 94.21954 assigned negative charge : -481.8619 centred at (gu) : 93.09937 98.92885 94.21241 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 64161 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27002 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 19530 mr = 43682 m= 1927 mr = 13585 m= 46 mr = 928 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 380 time to turn everything in is 0.3100000 number of dielectric boundary points 27465 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 362 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 23278 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) : 0.5375126 object centre at (A) : 21.21850 103.9515 132.4390 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0738502E-03 5.0877510E-03 midg,1,midg; midg,igrid,midg 2.7282471E-02 -1.3939387E-02 1,midg,midg; igrid,midg,midg -6.9495053E-03 -3.8194284E-03 gauss-seidel spectral radius is 0.9981417 estimated iterations to convergence 184 setup time was (sec) 0.5200000 now iterating at: 03:19:25 rms-change max change #iterations 3.322782 156.0938 at 10iterations 1.364335 53.12446 at 20iterations 0.5645039 24.14374 at 30iterations 0.2328131 8.290025 at 40iterations 9.6236803E-02 3.313261 at 50iterations 3.9668944E-02 1.396217 at 60iterations 1.6419001E-02 0.5707664 at 70iterations 6.8133702E-03 0.2389412 at 80iterations 2.8338842E-03 0.1083546 at 90iterations 1.1763839E-03 4.6466827E-02 at 100iterations 4.9750210E-04 1.9466400E-02 at 110iterations 2.1336005E-04 9.1362000E-03 at 120iterations finished qdiffx linear iterations at : 03:19:32 total time elapsed so far: 7.470000 # loops : 120 mean,max change (kT/e) : 2.1336005E-04 9.1362000E-03 energy calculations done at 7.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 03:19:33 7.620u 0.200s 0:08.16 95.8% 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 03:19:33 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 = 3185 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: 2.418807 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): -3.755000 46.19200 ymin,ymax (A): 70.83600 137.0670 zmin,zma (A): 102.6280 162.2500 x,y,z range (A): 49.94700 66.23100 59.62200 scale (grids/A): 2.418807 object centre (A): 21.21850 103.9515 132.4390 number of atom coordinates read : 3185 total number of charged atoms : 3046 net assigned charge : -5.999976 assigned positive charge : 475.8608 centred at (gu) : 94.82912 103.2591 96.32922 assigned negative charge : -481.8619 centred at (gu) : 94.64911 103.3932 96.31856 start vw surface at 0.1000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 149048 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27002 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 67865 mr = 106671 m= 18986 mr = 54024 m= 2976 mr = 14450 m= 175 mr = 1963 m= 3 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 1288 time to turn everything in is 0.8000000 number of dielectric boundary points 61860 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 24323 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) : 1.612538 object centre at (A) : 21.21850 103.9515 132.4390 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.5355017E-03 0.1892263 midg,1,midg; midg,igrid,midg 0.5072718 -0.3536761 1,midg,midg; igrid,midg,midg -9.9866182E-02 -4.8501935E-02 gauss-seidel spectral radius is 0.9991235 estimated iterations to convergence 267 setup time was (sec) 1.030000 now iterating at: 03:19:34 rms-change max change #iterations 8.722591 266.3458 at 10iterations 4.848814 132.9953 at 20iterations 2.690289 70.26283 at 30iterations 1.484866 32.28720 at 40iterations 0.8166441 19.02023 at 50iterations 0.4497009 9.533935 at 60iterations 0.2463466 5.038272 at 70iterations 0.1354167 2.967386 at 80iterations 7.4084841E-02 1.537699 at 90iterations 4.0535066E-02 0.9027081 at 100iterations 2.2160437E-02 0.5050821 at 110iterations 1.2120090E-02 0.2598772 at 120iterations 6.6654473E-03 0.1400890 at 130iterations 3.6463046E-03 7.5340748E-02 at 140iterations 1.9990350E-03 4.3029785E-02 at 150iterations 1.1001655E-03 2.1543503E-02 at 160iterations 6.1038672E-04 1.2977600E-02 at 170iterations 3.4124483E-04 7.0991516E-03 at 180iterations finished qdiffx linear iterations at : 03:19:45 total time elapsed so far: 12.28000 # loops : 180 mean,max change (kT/e) : 3.4124483E-04 7.0991516E-03 energy calculations done at 12.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.42000 DelPhi exited at 03:19:46 12.420u 0.199s 0:13.08 96.4% 0+0k 0+0io 0pf+0w