Sun Oct 9 06:35:44 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 Sun Oct 9 2011 at 06:35:44 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 = 1954 !!! WARNING: ASP 186 has a net charge of -2.0000 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: 0.6719897 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): 1.744000 44.74300 ymin,ymax (A): -9.298000 37.59500 zmin,zma (A): -24.50400 28.47300 x,y,z range (A): 42.99900 46.89300 52.97700 scale (grids/A): 0.6719897 object centre (A): 23.24350 14.14850 1.984500 number of atom coordinates read : 1954 total number of charged atoms : 1815 net assigned charge : 1.500010 assigned positive charge : 290.6370 centred at (gu) : 89.79787 89.34895 88.29684 assigned negative charge : -289.1372 centred at (gu) : 89.58231 89.22036 88.19364 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5915 nv = 96 ne = 84 npr = 40333 no. pairs analyzed = 40333 no. exposed pairs = 2431 no. arc points = 17258 no. surface atoms = 820 nbur = 1134 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 348 mr = 3217 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.2400000 number of dielectric boundary points 2995 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1612 ## 132 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 6779 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1260249E-08 1.8533587E-08 midg,1,midg; midg,igrid,midg -2.2849987E-08 2.7258675E-08 1,midg,midg; igrid,midg,midg -3.9432248E-08 4.5863707E-08 gauss-seidel spectral radius is 0.9884613 estimated iterations to convergence 76 setup time was (sec) 0.4800000 now iterating at: 06:35:44 rms-change max change #iterations 0.1529380 25.14582 at 10iterations 1.6754195E-02 2.490177 at 20iterations 1.8550584E-03 0.2973137 at 30iterations 1.9957396E-04 3.0494690E-02 at 40iterations 2.2040838E-05 3.4980774E-03 at 50iterations finished qdiffx linear iterations at : 06:35:47 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 2.2040838E-05 3.4980774E-03 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 06:35:48 3.349u 0.216s 0:03.83 92.6% 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 Sun Oct 9 2011 at 06:35:48 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 = 1954 !!! WARNING: ASP 186 has a net charge of -2.0000 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: 2.015969 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): 1.744000 44.74300 ymin,ymax (A): -9.298000 37.59500 zmin,zma (A): -24.50400 28.47300 x,y,z range (A): 42.99900 46.89300 52.97700 scale (grids/A): 2.015969 object centre (A): 23.24350 14.14850 1.984500 number of atom coordinates read : 1954 total number of charged atoms : 1815 net assigned charge : 1.500010 assigned positive charge : 290.6370 centred at (gu) : 89.39330 88.04684 84.89072 assigned negative charge : -289.1372 centred at (gu) : 88.74690 87.66107 84.58116 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 62895 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17258 grid for indexing accessible points = 1.400000 m= 23800 mr = 42850 m= 4268 mr = 17925 m= 330 mr = 2860 m= 3 mr = 130 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 933 time to turn everything in is 0.4800000 number of dielectric boundary points 27531 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 91 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 14347 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) : 0.6719897 object centre at (A) : 23.24350 14.14850 1.984500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1264942E-02 3.4024131E-02 midg,1,midg; midg,igrid,midg -1.8171849E-02 8.7883184E-03 1,midg,midg; igrid,midg,midg -2.9038228E-02 3.8173728E-02 gauss-seidel spectral radius is 0.9987099 estimated iterations to convergence 221 setup time was (sec) 0.7700000 now iterating at: 06:35:49 rms-change max change #iterations 4.018857 187.7258 at 10iterations 1.917154 68.40381 at 20iterations 0.9142520 32.37131 at 30iterations 0.4370527 15.15047 at 40iterations 0.2089881 7.307205 at 50iterations 0.1000612 3.218027 at 60iterations 4.7783002E-02 1.614720 at 70iterations 2.2860596E-02 0.7795955 at 80iterations 1.0858946E-02 0.4081707 at 90iterations 5.2214521E-03 0.1653061 at 100iterations 2.4980882E-03 8.7388039E-02 at 110iterations 1.1924354E-03 4.0536404E-02 at 120iterations finished qdiffx linear iterations at : 06:35:55 total time elapsed so far: 7.410000 # loops : 120 mean,max change (kT/e) : 1.1924354E-03 4.0536404E-02 energy calculations done at 7.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.590000 DelPhi exited at 06:35:56 7.593u 0.259s 0:08.15 96.1% 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 06:35:56 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 = 1954 !!! WARNING: ASP 186 has a net charge of -2.0000 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: 3.023954 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): 1.744000 44.74300 ymin,ymax (A): -9.298000 37.59500 zmin,zma (A): -24.50400 28.47300 x,y,z range (A): 42.99900 46.89300 52.97700 scale (grids/A): 3.023954 object centre (A): 23.24350 14.14850 1.984500 number of atom coordinates read : 1954 total number of charged atoms : 1815 net assigned charge : 1.500010 assigned positive charge : 290.6370 centred at (gu) : 89.08996 87.07019 82.33628 assigned negative charge : -289.1372 centred at (gu) : 88.12041 86.49158 81.87173 start vw surface at 0.1300000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 144870 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17258 grid for indexing accessible points = 1.400000 m= 75096 mr = 103438 m= 29545 mr = 61919 m= 8103 mr = 24290 m= 1383 mr = 6407 m= 100 mr = 944 m= 3 mr = 48 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 3057 time to turn everything in is 1.180000 number of dielectric boundary points 62055 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 14520 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) : 2.015969 object centre at (A) : 23.24350 14.14850 1.984500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6275444 0.7456464 midg,1,midg; midg,igrid,midg -0.1095016 0.1021794 1,midg,midg; igrid,midg,midg -0.2552258 0.3381744 gauss-seidel spectral radius is 0.9992625 estimated iterations to convergence 291 setup time was (sec) 1.510000 now iterating at: 06:35:57 rms-change max change #iterations 9.176520 411.1716 at 10iterations 5.298256 121.3277 at 20iterations 3.060957 66.09586 at 30iterations 1.766733 33.67931 at 40iterations 1.016252 22.33747 at 50iterations 0.5842652 12.48102 at 60iterations 0.3366819 6.148663 at 70iterations 0.1934959 3.586761 at 80iterations 0.1109316 2.664101 at 90iterations 6.3750863E-02 1.170244 at 100iterations 3.6673982E-02 0.7458038 at 110iterations 2.1099407E-02 0.3845180 at 120iterations 1.2054090E-02 0.2503352 at 130iterations 6.9407565E-03 0.1343679 at 140iterations 3.9900304E-03 7.7358246E-02 at 150iterations 2.2942871E-03 4.5331478E-02 at 160iterations 1.3135967E-03 2.3952484E-02 at 170iterations 7.5571117E-04 1.3477325E-02 at 180iterations finished qdiffx linear iterations at : 06:36:08 total time elapsed so far: 12.13000 # loops : 180 mean,max change (kT/e) : 7.5571117E-04 1.3477325E-02 energy calculations done at 12.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.31000 DelPhi exited at 06:36:09 12.314u 0.254s 0:12.84 97.8% 0+0k 0+0io 0pf+0w