Mon Oct 10 10:32:21 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 Mon Oct 10 2011 at 10:32:22 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 = 2888 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: 0.5604446 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): -22.07800 41.44300 ymin,ymax (A): -13.05600 45.71400 zmin,zma (A): -2.235000 51.07600 x,y,z range (A): 63.52100 58.77000 53.31100 scale (grids/A): 0.5604446 object centre (A): 9.682498 16.32900 24.42050 number of atom coordinates read : 2888 total number of charged atoms : 2735 net assigned charge : 5.000022 assigned positive charge : 421.9869 centred at (gu) : 92.28300 91.45577 86.76562 assigned negative charge : -416.9873 centred at (gu) : 92.31756 91.56970 86.55455 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6120 nv = 96 ne = 84 npr = 55921 no. pairs analyzed = 55921 no. exposed pairs = 4333 no. arc points = 31398 no. surface atoms = 1431 nbur = 1457 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 = 1.512000 m= 278 mr = 2708 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3673 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3094 ## 366 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7822 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.6270336E-09 1.2736554E-09 midg,1,midg; midg,igrid,midg 1.2656590E-09 -8.0127949E-10 1,midg,midg; igrid,midg,midg 5.7926947E-10 4.7321169E-10 gauss-seidel spectral radius is 0.9835861 estimated iterations to convergence 64 setup time was (sec) 0.5300000 now iterating at: 10:32:22 rms-change max change #iterations 7.8217998E-02 14.32720 at 10iterations 5.5214218E-03 1.142916 at 20iterations 4.0174229E-04 7.5038910E-02 at 30iterations 3.9787181E-05 5.7277679E-03 at 40iterations 7.3166648E-06 9.1362000E-04 at 50iterations finished qdiffx linear iterations at : 10:32:25 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 7.3166648E-06 9.1362000E-04 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 10:32:25 3.308u 0.200s 0:03.80 92.1% 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 Mon Oct 10 2011 at 10:32:25 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 = 2888 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: 1.681334 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): -22.07800 41.44300 ymin,ymax (A): -13.05600 45.71400 zmin,zma (A): -2.235000 51.07600 x,y,z range (A): 63.52100 58.77000 53.31100 scale (grids/A): 1.681334 object centre (A): 9.682498 16.32900 24.42050 number of atom coordinates read : 2888 total number of charged atoms : 2735 net assigned charge : 5.000022 assigned positive charge : 421.9869 centred at (gu) : 96.84846 94.36663 80.29650 assigned negative charge : -416.9873 centred at (gu) : 96.95235 94.70882 79.66354 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 66099 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31398 grid for indexing accessible points = 1.400000 m= 20148 mr = 40736 m= 2167 mr = 12624 m= 58 mr = 905 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 34207 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 306 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 21115 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) : 0.5604446 object centre at (A) : 9.682498 16.32900 24.42050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3885025E-02 1.2430910E-02 midg,1,midg; midg,igrid,midg 2.2890398E-02 2.3645125E-03 1,midg,midg; igrid,midg,midg -1.5322641E-02 -6.8669813E-03 gauss-seidel spectral radius is 0.9982905 estimated iterations to convergence 192 setup time was (sec) 0.7800000 now iterating at: 10:32:26 rms-change max change #iterations 3.383292 149.7431 at 10iterations 1.437037 58.95689 at 20iterations 0.6096413 20.60762 at 30iterations 0.2608041 9.048637 at 40iterations 0.1107265 4.276263 at 50iterations 4.7192216E-02 1.624410 at 60iterations 2.0143028E-02 0.7303133 at 70iterations 8.5702939E-03 0.3074517 at 80iterations 3.6723206E-03 0.1301632 at 90iterations 1.5674133E-03 5.3352356E-02 at 100iterations 6.7006046E-04 2.3740768E-02 at 110iterations 2.8856169E-04 1.0251045E-02 at 120iterations finished qdiffx linear iterations at : 10:32:33 total time elapsed so far: 7.290000 # loops : 120 mean,max change (kT/e) : 2.8856169E-04 1.0251045E-02 energy calculations done at 7.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 10:32:33 7.465u 0.208s 0:08.03 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 10:32:33 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 = 2888 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: 2.522001 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): -22.07800 41.44300 ymin,ymax (A): -13.05600 45.71400 zmin,zma (A): -2.235000 51.07600 x,y,z range (A): 63.52100 58.77000 53.31100 scale (grids/A): 2.522001 object centre (A): 9.682498 16.32900 24.42050 number of atom coordinates read : 2888 total number of charged atoms : 2735 net assigned charge : 5.000022 assigned positive charge : 421.9869 centred at (gu) : 100.2727 96.54984 75.44465 assigned negative charge : -416.9873 centred at (gu) : 100.4286 97.06300 74.49525 start vw surface at 0.1500000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 153059 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31398 grid for indexing accessible points = 1.400000 m= 68248 mr = 100876 m= 20153 mr = 50720 m= 3258 mr = 14100 m= 219 mr = 1879 m= 2 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.160000 number of dielectric boundary points 77285 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 21866 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) : 1.681334 object centre at (A) : 9.682498 16.32900 24.42050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1274135 0.1537262 midg,1,midg; midg,igrid,midg 0.4554966 2.8946368E-02 1,midg,midg; igrid,midg,midg -0.6304919 -0.1539631 gauss-seidel spectral radius is 0.9991775 estimated iterations to convergence 275 setup time was (sec) 1.480000 now iterating at: 10:32:35 rms-change max change #iterations 8.936618 283.9272 at 10iterations 5.171313 141.8001 at 20iterations 2.962234 82.67137 at 30iterations 1.689819 41.44344 at 40iterations 0.9568404 20.71998 at 50iterations 0.5398200 15.45579 at 60iterations 0.3041917 8.473757 at 70iterations 0.1706888 3.796758 at 80iterations 9.5361717E-02 2.302367 at 90iterations 5.3558968E-02 1.221495 at 100iterations 2.9899396E-02 0.7351427 at 110iterations 1.6703786E-02 0.3819914 at 120iterations 9.3483245E-03 0.2251434 at 130iterations 5.2065402E-03 0.1172771 at 140iterations 2.9082503E-03 6.4552307E-02 at 150iterations 1.6228867E-03 3.3885002E-02 at 160iterations 9.0454757E-04 1.8383026E-02 at 170iterations 5.0389877E-04 1.0489464E-02 at 180iterations finished qdiffx linear iterations at : 10:32:46 total time elapsed so far: 12.62000 # loops : 180 mean,max change (kT/e) : 5.0389877E-04 1.0489464E-02 energy calculations done at 12.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.79000 DelPhi exited at 10:32:47 12.789u 0.234s 0:13.36 97.3% 0+0k 0+0io 0pf+0w