Sun Oct 9 11:28:19 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 Sun Oct 9 2011 at 11:28:19 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2705 !!! WARNING: HIR 211 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5715478 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): 8.314000 60.20100 ymin,ymax (A): -30.22200 32.06500 zmin,zma (A): -9.243000 44.58000 x,y,z range (A): 51.88700 62.28700 53.82300 scale (grids/A): 0.5715478 object centre (A): 34.25750 0.9215012 17.66850 number of atom coordinates read : 2705 total number of charged atoms : 2563 net assigned charge : -0.9859792 assigned positive charge : 391.6854 centred at (gu) : 88.87316 90.24752 90.11372 assigned negative charge : -392.6727 centred at (gu) : 88.99671 90.20062 90.21162 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6142 nv = 96 ne = 84 npr = 52787 no. pairs analyzed = 52787 no. exposed pairs = 3779 no. arc points = 27670 no. surface atoms = 1264 nbur = 1441 mkacc time = 0.1400000 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 = 1.512000 m= 292 mr = 2937 m= 0 mr = 30 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3467 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2720 ## 274 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7577 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2009308E-09 -1.6750705E-09 midg,1,midg; midg,igrid,midg -8.2056600E-10 5.3292393E-10 1,midg,midg; igrid,midg,midg 2.1069904E-09 -1.5390013E-09 gauss-seidel spectral radius is 0.9842007 estimated iterations to convergence 65 setup time was (sec) 0.6600000 now iterating at: 11:28:20 rms-change max change #iterations 8.6522453E-02 15.89084 at 10iterations 6.2799607E-03 1.018616 at 20iterations 5.1863008E-04 8.1472397E-02 at 30iterations 6.6023604E-05 1.2880325E-02 at 40iterations 1.3397996E-05 2.5043488E-03 at 50iterations finished qdiffx linear iterations at : 11:28:25 total time elapsed so far: 5.320000 # loops : 50 mean,max change (kT/e) : 1.3397996E-05 2.5043488E-03 energy calculations done at 5.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.480000 DelPhi exited at 11:28:26 5.488u 0.496s 0:06.25 95.5% 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 Sun Oct 9 2011 at 11:28:26 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2705 !!! WARNING: HIR 211 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.714643 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): 8.314000 60.20100 ymin,ymax (A): -30.22200 32.06500 zmin,zma (A): -9.243000 44.58000 x,y,z range (A): 51.88700 62.28700 53.82300 scale (grids/A): 1.714643 object centre (A): 34.25750 0.9215012 17.66850 number of atom coordinates read : 2705 total number of charged atoms : 2563 net assigned charge : -0.9859792 assigned positive charge : 391.6854 centred at (gu) : 86.61846 90.74184 90.34039 assigned negative charge : -392.6727 centred at (gu) : 86.98988 90.60164 90.63477 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 66792 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27670 grid for indexing accessible points = 1.400000 m= 21298 mr = 43166 m= 2914 mr = 14327 m= 117 mr = 1629 m= 0 mr = 20 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 31979 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 219 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 19882 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) : 0.5715478 object centre at (A) : 34.25750 0.9215012 17.66850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6041880E-02 -1.6600400E-02 midg,1,midg; midg,igrid,midg -5.8072014E-03 -7.3792436E-03 1,midg,midg; igrid,midg,midg 9.8705003E-03 -1.1135492E-02 gauss-seidel spectral radius is 0.9983646 estimated iterations to convergence 196 setup time was (sec) 0.9500000 now iterating at: 11:28:27 rms-change max change #iterations 3.464245 162.1441 at 10iterations 1.500612 64.18623 at 20iterations 0.6526731 22.28652 at 30iterations 0.2823336 11.60240 at 40iterations 0.1230819 4.367207 at 50iterations 5.3632006E-02 1.974661 at 60iterations 2.3326896E-02 0.7520447 at 70iterations 1.0184561E-02 0.3441868 at 80iterations 4.4335104E-03 0.1528294 at 90iterations 1.9416525E-03 7.0529938E-02 at 100iterations 8.4865134E-04 3.1230927E-02 at 110iterations 3.7199858E-04 1.3595700E-02 at 120iterations finished qdiffx linear iterations at : 11:28:39 total time elapsed so far: 12.69000 # loops : 120 mean,max change (kT/e) : 3.7199858E-04 1.3595700E-02 energy calculations done at 12.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.87000 DelPhi exited at 11:28:39 12.875u 0.535s 0:13.79 97.1% 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 Sun Oct 9 2011 at 11:28:39 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2705 !!! WARNING: HIR 211 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.571965 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): 8.314000 60.20100 ymin,ymax (A): -30.22200 32.06500 zmin,zma (A): -9.243000 44.58000 x,y,z range (A): 51.88700 62.28700 53.82300 scale (grids/A): 2.571965 object centre (A): 34.25750 0.9215012 17.66850 number of atom coordinates read : 2705 total number of charged atoms : 2563 net assigned charge : -0.9859792 assigned positive charge : 391.6854 centred at (gu) : 84.92771 91.11243 90.51032 assigned negative charge : -392.6727 centred at (gu) : 85.48480 90.90251 90.95228 start vw surface at 0.1200000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 154767 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27670 grid for indexing accessible points = 1.400000 m= 70744 mr = 106134 m= 23067 mr = 54792 m= 5134 mr = 17333 m= 550 mr = 3607 m= 9 mr = 291 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.440000 number of dielectric boundary points 72114 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 20490 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) : 1.714643 object centre at (A) : 34.25750 0.9215012 17.66850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2314843 -0.1571010 midg,1,midg; midg,igrid,midg -0.1523895 -0.1725479 1,midg,midg; igrid,midg,midg 0.1456360 -0.2123824 gauss-seidel spectral radius is 0.9991974 estimated iterations to convergence 279 setup time was (sec) 1.840000 now iterating at: 11:28:42 rms-change max change #iterations 8.813833 256.3453 at 10iterations 5.119287 118.7737 at 20iterations 2.938394 67.88477 at 30iterations 1.681541 40.87577 at 40iterations 0.9570602 21.04977 at 50iterations 0.5421539 12.78760 at 60iterations 0.3070064 5.973980 at 70iterations 0.1735107 3.668196 at 80iterations 9.7856797E-02 1.930252 at 90iterations 5.5064164E-02 1.180271 at 100iterations 3.0995836E-02 0.7409916 at 110iterations 1.7431047E-02 0.4017029 at 120iterations 9.7969081E-03 0.2247505 at 130iterations 5.5078869E-03 0.1146431 at 140iterations 3.0996099E-03 6.3320160E-02 at 150iterations 1.7428875E-03 3.4263611E-02 at 160iterations 9.8126219E-04 2.5516510E-02 at 170iterations 5.5404560E-04 1.2455940E-02 at 180iterations finished qdiffx linear iterations at : 11:29:02 total time elapsed so far: 21.73000 # loops : 180 mean,max change (kT/e) : 5.5404560E-04 1.2455940E-02 energy calculations done at 21.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.90000 DelPhi exited at 11:29:02 21.907u 0.562s 0:22.74 98.7% 0+0k 0+0io 0pf+0w