Sat Oct 15 14:08:56 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 Sat Oct 15 2011 at 14:08:57 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4677 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.5099337 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): -15.86300 37.53900 ymin,ymax (A): -30.96300 34.85300 zmin,zma (A): -3.897000 65.91600 x,y,z range (A): 53.40200 65.81600 69.81300 scale (grids/A): 0.5099337 object centre (A): 10.83800 1.945000 31.00950 number of atom coordinates read : 4677 total number of charged atoms : 4432 net assigned charge : 6.800032 assigned positive charge : 703.8586 centred at (gu) : 89.50168 90.62484 88.03010 assigned negative charge : -697.0627 centred at (gu) : 89.40601 90.66769 87.99944 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7836 nv = 96 ne = 84 npr = 92515 no. pairs analyzed = 92515 no. exposed pairs = 6050 no. arc points = 42092 no. surface atoms = 2028 nbur = 2649 mkacc time = 0.1700000 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 = 1.680000 m= 302 mr = 3983 m= 0 mr = 5 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4150 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4033 ## 576 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 10301 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3257081E-11 1.0315537E-10 midg,1,midg; midg,igrid,midg 1.7085190E-10 -1.0785839E-11 1,midg,midg; igrid,midg,midg -1.6075741E-10 2.8760519E-10 gauss-seidel spectral radius is 0.9803332 estimated iterations to convergence 59 setup time was (sec) 0.5300000 now iterating at: 14:08:57 rms-change max change #iterations 6.7644469E-02 10.07430 at 10iterations 3.8986253E-03 0.7102394 at 20iterations 4.2589894E-04 5.9499741E-02 at 30iterations 1.5184171E-04 2.6246309E-02 at 40iterations 6.5053711E-05 1.1914492E-02 at 50iterations finished qdiffx linear iterations at : 14:09:03 total time elapsed so far: 3.650000 # loops : 50 mean,max change (kT/e) : 6.5053711E-05 1.1914492E-02 energy calculations done at 3.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.790000 DelPhi exited at 14:09:03 3.793u 0.256s 0:06.98 57.8% 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 Sat Oct 15 2011 at 14:09:04 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4677 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.529801 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): -15.86300 37.53900 ymin,ymax (A): -30.96300 34.85300 zmin,zma (A): -3.897000 65.91600 x,y,z range (A): 53.40200 65.81600 69.81300 scale (grids/A): 1.529801 object centre (A): 10.83800 1.945000 31.00950 number of atom coordinates read : 4677 total number of charged atoms : 4432 net assigned charge : 6.800032 assigned positive charge : 703.8586 centred at (gu) : 88.50350 91.87310 84.08865 assigned negative charge : -697.0627 centred at (gu) : 88.21744 92.00277 83.99780 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 88669 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42092 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 26118 mr = 60443 m= 2280 mr = 17258 m= 58 mr = 927 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.4500000 number of dielectric boundary points 38497 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 563 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 33310 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) : 0.5099337 object centre at (A) : 10.83800 1.945000 31.00950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9826452E-03 2.1186328E-02 midg,1,midg; midg,igrid,midg -4.0352240E-04 -9.9548222E-03 1,midg,midg; igrid,midg,midg -5.7709625E-04 9.9117961E-03 gauss-seidel spectral radius is 0.9981052 estimated iterations to convergence 183 setup time was (sec) 0.7000000 now iterating at: 14:09:07 rms-change max change #iterations 3.761779 153.5898 at 10iterations 1.537335 53.30088 at 20iterations 0.6311677 22.10931 at 30iterations 0.2579505 8.476050 at 40iterations 0.1060863 3.773804 at 50iterations 4.3570064E-02 1.382826 at 60iterations 1.7838676E-02 0.5410366 at 70iterations 7.3646903E-03 0.2329559 at 80iterations 3.0607467E-03 0.1012955 at 90iterations 1.2960372E-03 4.6613693E-02 at 100iterations 5.8027258E-04 2.1817684E-02 at 110iterations 2.9869133E-04 1.1113167E-02 at 120iterations finished qdiffx linear iterations at : 14:09:19 total time elapsed so far: 8.510000 # loops : 120 mean,max change (kT/e) : 2.9869133E-04 1.1113167E-02 energy calculations done at 8.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.640000 DelPhi exited at 14:09:20 8.647u 0.292s 0:15.69 56.9% 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 Sat Oct 15 2011 at 14:09:20 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4677 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 2.294701 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): -15.86300 37.53900 ymin,ymax (A): -30.96300 34.85300 zmin,zma (A): -3.897000 65.91600 x,y,z range (A): 53.40200 65.81600 69.81300 scale (grids/A): 2.294701 object centre (A): 10.83800 1.945000 31.00950 number of atom coordinates read : 4677 total number of charged atoms : 4432 net assigned charge : 6.800032 assigned positive charge : 703.8586 centred at (gu) : 87.75506 92.80936 81.13275 assigned negative charge : -697.0627 centred at (gu) : 87.32613 93.00411 80.99683 start vw surface at 0.1100000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 206866 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42092 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 93262 mr = 149186 m= 23731 mr = 72399 m= 3329 mr = 16806 m= 197 mr = 1971 m= 2 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 61 time to turn everything in is 1.070000 number of dielectric boundary points 86952 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 71 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 35341 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) : 1.529801 object centre at (A) : 10.83800 1.945000 31.00950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1246100 0.4637035 midg,1,midg; midg,igrid,midg -6.1321840E-02 -0.2621637 1,midg,midg; igrid,midg,midg -6.7097964E-03 0.1478234 gauss-seidel spectral radius is 0.9991599 estimated iterations to convergence 272 setup time was (sec) 1.340000 now iterating at: 14:09:22 rms-change max change #iterations 10.18014 270.1772 at 10iterations 5.815922 152.7000 at 20iterations 3.303255 70.47636 at 30iterations 1.861336 53.37107 at 40iterations 1.046434 23.18273 at 50iterations 0.5868620 11.77163 at 60iterations 0.3289030 6.370514 at 70iterations 0.1837157 4.201130 at 80iterations 0.1025590 2.053875 at 90iterations 5.7113420E-02 1.098000 at 100iterations 3.1700738E-02 0.5865299 at 110iterations 1.7658720E-02 0.3368092 at 120iterations 9.8304572E-03 0.2028702 at 130iterations 5.4574287E-03 0.1122780 at 140iterations 3.0344462E-03 5.4298401E-02 at 150iterations 1.6914097E-03 3.4584045E-02 at 160iterations 9.4698236E-04 2.1192551E-02 at 170iterations 5.3546147E-04 1.0752678E-02 at 180iterations finished qdiffx linear iterations at : 14:09:40 total time elapsed so far: 14.12000 # loops : 180 mean,max change (kT/e) : 5.3546147E-04 1.0752678E-02 energy calculations done at 14.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.25000 DelPhi exited at 14:09:41 14.250u 0.314s 0:20.76 70.1% 0+0k 0+0io 0pf+0w