Sun Oct 9 03:08:59 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 03:08:59 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4419 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.4437741 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): 15.71900 95.94000 ymin,ymax (A): -3.443000 54.88500 zmin,zma (A): 156.3790 222.6860 x,y,z range (A): 80.22100 58.32800 66.30699 scale (grids/A): 0.4437741 object centre (A): 55.82950 25.72100 189.5325 number of atom coordinates read : 4419 total number of charged atoms : 4187 net assigned charge : 19.00002 assigned positive charge : 643.9024 centred at (gu) : 94.85770 91.03845 88.50520 assigned negative charge : -624.9068 centred at (gu) : 94.89781 91.03046 88.55209 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 5242 nv = 96 ne = 84 npr = 89988 no. pairs analyzed = 89988 no. exposed pairs = 5568 no. arc points = 38905 no. surface atoms = 1897 nbur = 2522 mkacc time = 0.1900000 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 = 1.904000 m= 126 mr = 2511 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 2857 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3218 ## 622 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 7063 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9264125E-11 3.0998270E-12 midg,1,midg; midg,igrid,midg 5.8467432E-12 1.2495545E-11 1,midg,midg; igrid,midg,midg 2.9151111E-12 2.1922870E-11 gauss-seidel spectral radius is 0.9740729 estimated iterations to convergence 52 setup time was (sec) 0.6300000 now iterating at: 03:09:00 rms-change max change #iterations 3.0991903E-02 6.380676 at 10iterations 2.6229182E-03 0.4668293 at 20iterations 5.7965307E-04 0.1067696 at 30iterations 1.4084594E-04 2.6794434E-02 at 40iterations 3.4396377E-05 6.6566467E-03 at 50iterations finished qdiffx linear iterations at : 03:09:03 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 3.4396377E-05 6.6566467E-03 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 03:09:03 3.325u 0.165s 0:03.76 92.5% 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 03:09:03 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4419 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.331322 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): 15.71900 95.94000 ymin,ymax (A): -3.443000 54.88500 zmin,zma (A): 156.3790 222.6860 x,y,z range (A): 80.22100 58.32800 66.30699 scale (grids/A): 1.331322 object centre (A): 55.82950 25.72100 189.5325 number of atom coordinates read : 4419 total number of charged atoms : 4187 net assigned charge : 19.00002 assigned positive charge : 643.9024 centred at (gu) : 104.5714 93.11327 85.51425 assigned negative charge : -624.9068 centred at (gu) : 104.6931 93.09091 85.65617 start vw surface at 0.2000000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 60893 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38905 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 14383 mr = 40247 m= 752 mr = 8755 m= 7 mr = 191 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 474 time to turn everything in is 0.4900000 number of dielectric boundary points 26842 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 623 ## 15 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 29563 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) : 0.4437741 object centre at (A) : 55.82950 25.72100 189.5325 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5011779E-03 2.0299198E-03 midg,1,midg; midg,igrid,midg 9.7036076E-04 1.4822283E-03 1,midg,midg; igrid,midg,midg 3.4293775E-03 2.1811256E-02 gauss-seidel spectral radius is 0.9973390 estimated iterations to convergence 155 setup time was (sec) 0.7500000 now iterating at: 03:09:04 rms-change max change #iterations 2.482754 116.0047 at 10iterations 0.8622708 35.34889 at 20iterations 0.3008743 11.64899 at 30iterations 0.1049827 3.883963 at 40iterations 3.6876775E-02 1.467167 at 50iterations 1.3049311E-02 0.5326133 at 60iterations 4.8176842E-03 0.2028179 at 70iterations 1.9292061E-03 7.8542709E-02 at 80iterations 8.8128122E-04 3.7738800E-02 at 90iterations 4.6234287E-04 1.9836426E-02 at 100iterations 2.6397716E-04 1.1142731E-02 at 110iterations 1.5706167E-04 6.6623688E-03 at 120iterations finished qdiffx linear iterations at : 03:09:10 total time elapsed so far: 6.880000 # loops : 120 mean,max change (kT/e) : 1.5706167E-04 6.6623688E-03 energy calculations done at 6.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.070000 DelPhi exited at 03:09:11 7.071u 0.182s 0:07.53 96.2% 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 03:09:11 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4419 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.996983 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): 15.71900 95.94000 ymin,ymax (A): -3.443000 54.88500 zmin,zma (A): 156.3790 222.6860 x,y,z range (A): 80.22100 58.32800 66.30699 scale (grids/A): 1.996983 object centre (A): 55.82950 25.72100 189.5325 number of atom coordinates read : 4419 total number of charged atoms : 4187 net assigned charge : 19.00002 assigned positive charge : 643.9024 centred at (gu) : 111.8570 94.66948 83.27090 assigned negative charge : -624.9068 centred at (gu) : 112.0396 94.63638 83.48415 start vw surface at 0.1800000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 142913 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38905 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.764000 m= 55411 mr = 100358 m= 10373 mr = 41373 m= 793 mr = 6718 m= 14 mr = 325 m= 0 mr = 0 time to grow re-entrant surface = 0.5700000 no. cavity mid-points inaccessible to solvent = 1663 time to turn everything in is 1.030000 number of dielectric boundary points 60730 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 33138 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) : 1.331322 object centre at (A) : 55.82950 25.72100 189.5325 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.3416641E-02 4.8555814E-02 midg,1,midg; midg,igrid,midg 2.0541692E-02 2.1713261E-02 1,midg,midg; igrid,midg,midg 5.2351490E-02 0.3669738 gauss-seidel spectral radius is 0.9988711 estimated iterations to convergence 236 setup time was (sec) 1.310000 now iterating at: 03:09:12 rms-change max change #iterations 7.423363 232.7875 at 10iterations 3.853187 102.6426 at 20iterations 1.993344 59.84595 at 30iterations 1.026379 27.58830 at 40iterations 0.5244185 15.29114 at 50iterations 0.2681341 7.277618 at 60iterations 0.1361144 3.203938 at 70iterations 6.9129102E-02 1.832971 at 80iterations 3.5137542E-02 0.8529510 at 90iterations 1.7802956E-02 0.4179039 at 100iterations 9.0579949E-03 0.2050114 at 110iterations 4.6217963E-03 0.1062050 at 120iterations 2.3590794E-03 5.3718090E-02 at 130iterations 1.2232937E-03 2.8509140E-02 at 140iterations 6.4573193E-04 1.9174576E-02 at 150iterations 3.5265743E-04 9.4652176E-03 at 160iterations 2.0255795E-04 5.0964355E-03 at 170iterations 1.2276691E-04 3.1623840E-03 at 180iterations finished qdiffx linear iterations at : 03:09:22 total time elapsed so far: 10.82000 # loops : 180 mean,max change (kT/e) : 1.2276691E-04 3.1623840E-03 energy calculations done at 10.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.00000 DelPhi exited at 03:09:22 10.999u 0.193s 0:11.47 97.4% 0+0k 0+0io 0pf+0w