Mon Oct 10 19:32:10 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 19:32:10 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 = 2419 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: 0.6004081 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): -11.25800 48.03500 ymin,ymax (A): 60.49900 115.5460 zmin,zma (A): 44.04900 87.68400 x,y,z range (A): 59.29300 55.04701 43.63500 scale (grids/A): 0.6004081 object centre (A): 18.38850 88.02250 65.86650 number of atom coordinates read : 2419 total number of charged atoms : 2280 net assigned charge : 7.7784061E-06 assigned positive charge : 364.7697 centred at (gu) : 87.76257 91.25545 91.32597 assigned negative charge : -364.7705 centred at (gu) : 87.82238 91.35390 91.45010 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5882 nv = 96 ne = 84 npr = 48470 no. pairs analyzed = 48470 no. exposed pairs = 3042 no. arc points = 20896 no. surface atoms = 1019 nbur = 1400 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 300 mr = 3231 m= 2 mr = 27 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 0.2600000 number of dielectric boundary points 2926 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2077 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7193 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1526819E-09 -5.8088809E-09 midg,1,midg; midg,igrid,midg 2.5582416E-09 -4.4995838E-09 1,midg,midg; igrid,midg,midg 3.5577907E-09 -1.2039012E-09 gauss-seidel spectral radius is 0.9856274 estimated iterations to convergence 68 setup time was (sec) 0.4900000 now iterating at: 19:32:11 rms-change max change #iterations 0.1036233 17.56093 at 10iterations 8.8902246E-03 1.523273 at 20iterations 8.2003797E-04 0.1241226 at 30iterations 1.0415065E-04 2.1752357E-02 at 40iterations 2.2440106E-05 4.8880577E-03 at 50iterations finished qdiffx linear iterations at : 19:32:14 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 2.2440106E-05 4.8880577E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 19:32:14 3.402u 0.194s 0:03.87 92.7% 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 19:32:14 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 = 2419 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.801224 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): -11.25800 48.03500 ymin,ymax (A): 60.49900 115.5460 zmin,zma (A): 44.04900 87.68400 x,y,z range (A): 59.29300 55.04701 43.63500 scale (grids/A): 1.801224 object centre (A): 18.38850 88.02250 65.86650 number of atom coordinates read : 2419 total number of charged atoms : 2280 net assigned charge : 7.7784061E-06 assigned positive charge : 364.7697 centred at (gu) : 83.28721 93.76586 93.97720 assigned negative charge : -364.7705 centred at (gu) : 83.46688 94.06155 94.34974 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 63893 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20896 grid for indexing accessible points = 1.400000 m= 22417 mr = 44582 m= 3081 mr = 16359 m= 132 mr = 1764 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 413 time to turn everything in is 0.5100000 number of dielectric boundary points 26796 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 169 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 17830 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) : 0.6004081 object centre at (A) : 18.38850 88.02250 65.86650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0429682E-03 -6.4934194E-03 midg,1,midg; midg,igrid,midg 2.2377675E-02 -1.6316596E-02 1,midg,midg; igrid,midg,midg -1.4053021E-02 -1.3549895E-02 gauss-seidel spectral radius is 0.9984538 estimated iterations to convergence 202 setup time was (sec) 0.8000000 now iterating at: 19:32:15 rms-change max change #iterations 3.650961 179.7686 at 10iterations 1.621372 68.18370 at 20iterations 0.7244018 24.76300 at 30iterations 0.3230552 11.38238 at 40iterations 0.1437177 4.917564 at 50iterations 6.4165108E-02 2.566700 at 60iterations 2.8585661E-02 0.9864807 at 70iterations 1.2841754E-02 0.4189816 at 80iterations 5.7378230E-03 0.2054062 at 90iterations 2.5635187E-03 9.0787888E-02 at 100iterations 1.1573968E-03 4.0788651E-02 at 110iterations 5.2493962E-04 1.9541264E-02 at 120iterations finished qdiffx linear iterations at : 19:32:22 total time elapsed so far: 7.400000 # loops : 120 mean,max change (kT/e) : 5.2493962E-04 1.9541264E-02 energy calculations done at 7.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.580000 DelPhi exited at 19:32:22 7.579u 0.272s 0:08.28 94.6% 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 Mon Oct 10 2011 at 19:32:23 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 = 2419 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.701837 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): -11.25800 48.03500 ymin,ymax (A): 60.49900 115.5460 zmin,zma (A): 44.04900 87.68400 x,y,z range (A): 59.29300 55.04701 43.63500 scale (grids/A): 2.701837 object centre (A): 18.38850 88.02250 65.86650 number of atom coordinates read : 2419 total number of charged atoms : 2280 net assigned charge : 7.7784061E-06 assigned positive charge : 364.7697 centred at (gu) : 79.93065 95.64865 95.96555 assigned negative charge : -364.7705 centred at (gu) : 80.20025 96.09229 96.52454 start vw surface at 0.1600000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 148002 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20896 grid for indexing accessible points = 1.400000 m= 73518 mr = 108317 m= 25395 mr = 59704 m= 5356 mr = 20185 m= 623 mr = 3877 m= 35 mr = 377 m= 0 mr = 15 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 1397 time to turn everything in is 1.110000 number of dielectric boundary points 60454 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 18236 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) : 1.801224 object centre at (A) : 18.38850 88.02250 65.86650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.1623012E-02 -4.1952886E-02 midg,1,midg; midg,igrid,midg 0.3346425 -0.2618891 1,midg,midg; igrid,midg,midg -0.2338970 -8.1269564E-03 gauss-seidel spectral radius is 0.9992031 estimated iterations to convergence 280 setup time was (sec) 1.380000 now iterating at: 19:32:24 rms-change max change #iterations 8.898919 278.7303 at 10iterations 5.124815 114.4245 at 20iterations 2.914746 68.08790 at 30iterations 1.659336 36.01823 at 40iterations 0.9388435 20.69379 at 50iterations 0.5307294 11.10783 at 60iterations 0.3005810 6.529333 at 70iterations 0.1693065 3.245625 at 80iterations 9.5708810E-02 2.056126 at 90iterations 5.3788520E-02 1.300295 at 100iterations 3.0223394E-02 0.6233578 at 110iterations 1.7017175E-02 0.3649273 at 120iterations 9.5908772E-03 0.2226830 at 130iterations 5.3935004E-03 0.1144104 at 140iterations 3.0354762E-03 6.2068701E-02 at 150iterations 1.7086817E-03 3.8539886E-02 at 160iterations 9.6195214E-04 2.0193100E-02 at 170iterations 5.4184318E-04 1.0931015E-02 at 180iterations finished qdiffx linear iterations at : 19:32:34 total time elapsed so far: 10.79000 # loops : 180 mean,max change (kT/e) : 5.4184318E-04 1.0931015E-02 energy calculations done at 10.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.97000 DelPhi exited at 19:32:35 10.969u 0.173s 0:11.90 93.5% 0+0k 0+0io 0pf+0w