Sun Oct 9 23:03:21 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 Sun Oct 9 2011 at 23:03:21 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4786 !!! WARNING: GLM 297 has a net charge of -0.6000 !!! WARNING: HIZ 301 has a net charge of 0.2000 !!! WARNING: ZN7 776 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: 0.5200876 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): -8.071000 46.53000 ymin,ymax (A): -30.17800 38.27200 zmin,zma (A): -0.1610000 65.46000 x,y,z range (A): 54.60100 68.45000 65.62100 scale (grids/A): 0.5200876 object centre (A): 19.22950 4.047002 32.64950 number of atom coordinates read : 4786 total number of charged atoms : 4624 net assigned charge : 13.50002 assigned positive charge : 733.2258 centred at (gu) : 89.56248 89.83592 88.27237 assigned negative charge : -719.7314 centred at (gu) : 89.48344 89.76750 88.09956 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7300 nv = 96 ne = 84 npr = 102489 no. pairs analyzed = 102489 no. exposed pairs = 5661 no. arc points = 39493 no. surface atoms = 1901 nbur = 2885 mkacc time = 0.2100000 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= 281 mr = 3612 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 3964 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3998 ## 604 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 10585 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.1159705E-10 6.1587541E-10 midg,1,midg; midg,igrid,midg 3.8651811E-11 5.4444182E-10 1,midg,midg; igrid,midg,midg -6.6116375E-12 5.4358584E-10 gauss-seidel spectral radius is 0.9810729 estimated iterations to convergence 60 setup time was (sec) 0.6500000 now iterating at: 23:03:22 rms-change max change #iterations 7.5629361E-02 11.50808 at 10iterations 4.4010640E-03 0.7028055 at 20iterations 3.8792141E-04 7.0396423E-02 at 30iterations 9.4941694E-05 2.0112991E-02 at 40iterations 3.0883723E-05 6.7443848E-03 at 50iterations finished qdiffx linear iterations at : 23:03:25 total time elapsed so far: 3.040000 # loops : 50 mean,max change (kT/e) : 3.0883723E-05 6.7443848E-03 energy calculations done at 3.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.220000 DelPhi exited at 23:03:25 3.222u 0.133s 0:03.65 91.7% 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 Sun Oct 9 2011 at 23:03:25 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4786 !!! WARNING: GLM 297 has a net charge of -0.6000 !!! WARNING: HIZ 301 has a net charge of 0.2000 !!! WARNING: ZN7 776 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: 1.560263 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): -8.071000 46.53000 ymin,ymax (A): -30.17800 38.27200 zmin,zma (A): -0.1610000 65.46000 x,y,z range (A): 54.60100 68.45000 65.62100 scale (grids/A): 1.560263 object centre (A): 19.22950 4.047002 32.64950 number of atom coordinates read : 4786 total number of charged atoms : 4624 net assigned charge : 13.50002 assigned positive charge : 733.2258 centred at (gu) : 88.68555 89.50581 84.81517 assigned negative charge : -719.7314 centred at (gu) : 88.44995 89.30228 84.29853 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 83673 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39493 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 20381 mr = 56071 m= 1732 mr = 12189 m= 30 mr = 593 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 144 time to turn everything in is 0.5800000 number of dielectric boundary points 36963 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 558 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 34933 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) : 0.5200876 object centre at (A) : 19.22950 4.047002 32.64950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7488008E-02 2.9009892E-02 midg,1,midg; midg,igrid,midg 2.3221381E-03 1.8342305E-02 1,midg,midg; igrid,midg,midg -5.7386770E-03 3.9620982E-03 gauss-seidel spectral radius is 0.9981627 estimated iterations to convergence 185 setup time was (sec) 0.8500000 now iterating at: 23:03:26 rms-change max change #iterations 3.930726 170.1731 at 10iterations 1.623853 58.53055 at 20iterations 0.6742097 22.90596 at 30iterations 0.2793598 8.365524 at 40iterations 0.1158338 3.574381 at 50iterations 4.7838029E-02 1.602578 at 60iterations 1.9927956E-02 0.7521057 at 70iterations 8.3009014E-03 0.2713890 at 80iterations 3.4536275E-03 0.1186380 at 90iterations 1.4525690E-03 5.1628113E-02 at 100iterations 6.2328042E-04 1.9592285E-02 at 110iterations 2.7700129E-04 1.0510445E-02 at 120iterations finished qdiffx linear iterations at : 23:03:32 total time elapsed so far: 6.800000 # loops : 120 mean,max change (kT/e) : 2.7700129E-04 1.0510445E-02 energy calculations done at 6.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.970000 DelPhi exited at 23:03:33 6.972u 0.175s 0:07.48 95.4% 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 23:03:33 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4786 !!! WARNING: GLM 297 has a net charge of -0.6000 !!! WARNING: HIZ 301 has a net charge of 0.2000 !!! WARNING: ZN7 776 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: 2.340394 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): -8.071000 46.53000 ymin,ymax (A): -30.17800 38.27200 zmin,zma (A): -0.1610000 65.46000 x,y,z range (A): 54.60100 68.45000 65.62100 scale (grids/A): 2.340394 object centre (A): 19.22950 4.047002 32.64950 number of atom coordinates read : 4786 total number of charged atoms : 4624 net assigned charge : 13.50002 assigned positive charge : 733.2258 centred at (gu) : 88.02792 89.25827 82.22222 assigned negative charge : -719.7314 centred at (gu) : 87.67468 88.95322 81.44760 start vw surface at 0.1800000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 196236 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39493 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 75438 mr = 139497 m= 16819 mr = 55901 m= 2205 mr = 10898 m= 89 mr = 1142 m= 2 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 444 time to turn everything in is 1.320000 number of dielectric boundary points 83336 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 52 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 36892 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) : 1.560263 object centre at (A) : 19.22950 4.047002 32.64950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7426218 0.4014887 midg,1,midg; midg,igrid,midg 0.1274023 0.2853731 1,midg,midg; igrid,midg,midg -0.1078639 4.3889686E-02 gauss-seidel spectral radius is 0.9991716 estimated iterations to convergence 274 setup time was (sec) 1.610000 now iterating at: 23:03:34 rms-change max change #iterations 10.69440 316.8785 at 10iterations 6.189869 171.0480 at 20iterations 3.540049 86.96480 at 30iterations 2.023173 44.35414 at 40iterations 1.144492 25.85559 at 50iterations 0.6469454 12.27177 at 60iterations 0.3645462 7.021574 at 70iterations 0.2044923 3.814843 at 80iterations 0.1146041 2.241906 at 90iterations 6.4180560E-02 1.393181 at 100iterations 3.5916567E-02 0.7025824 at 110iterations 2.0076565E-02 0.4162745 at 120iterations 1.1219756E-02 0.2196999 at 130iterations 6.2737130E-03 0.1217537 at 140iterations 3.5117855E-03 6.7882538E-02 at 150iterations 1.9655663E-03 3.4017980E-02 at 160iterations 1.1078774E-03 2.0603180E-02 at 170iterations 6.2677485E-04 1.2371063E-02 at 180iterations finished qdiffx linear iterations at : 23:03:44 total time elapsed so far: 11.17000 # loops : 180 mean,max change (kT/e) : 6.2677485E-04 1.2371063E-02 energy calculations done at 11.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.35000 DelPhi exited at 23:03:44 11.349u 0.174s 0:11.79 97.6% 0+0k 0+0io 0pf+0w