Sun Oct 9 01:47:50 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 01:47:50 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3463 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 0.5475659 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): -40.81000 16.36300 ymin,ymax (A): -12.06800 49.52300 zmin,zma (A): -51.62200 13.39300 x,y,z range (A): 57.17300 61.59100 65.01500 scale (grids/A): 0.5475659 object centre (A): -12.22350 18.72750 -19.11450 number of atom coordinates read : 3463 total number of charged atoms : 3319 net assigned charge : 11.22603 assigned positive charge : 513.7744 centred at (gu) : 89.59973 90.11332 91.60398 assigned negative charge : -502.5501 centred at (gu) : 89.69542 90.03501 91.82807 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6989 nv = 96 ne = 84 npr = 67047 no. pairs analyzed = 67047 no. exposed pairs = 4577 no. arc points = 33498 no. surface atoms = 1533 nbur = 1930 mkacc time = 0.1400000 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 = 1.540000 m= 278 mr = 3479 m= 0 mr = 14 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3774 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3317 ## 405 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 9013 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6889995E-09 -1.6122716E-09 midg,1,midg; midg,igrid,midg 1.4120347E-10 1.4269518E-09 1,midg,midg; igrid,midg,midg 1.6804530E-09 6.1054412E-12 gauss-seidel spectral radius is 0.9828546 estimated iterations to convergence 63 setup time was (sec) 0.7100000 now iterating at: 01:47:51 rms-change max change #iterations 7.8299329E-02 12.40277 at 10iterations 5.2698725E-03 0.7870513 at 20iterations 3.6430368E-04 6.5769196E-02 at 30iterations 3.0423080E-05 4.1351318E-03 at 40iterations 3.8882117E-06 3.9672852E-04 at 50iterations finished qdiffx linear iterations at : 01:47:54 total time elapsed so far: 3.510000 # loops : 50 mean,max change (kT/e) : 3.8882117E-06 3.9672852E-04 energy calculations done at 3.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.680000 DelPhi exited at 01:47:55 3.681u 0.346s 0:04.30 93.4% 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 01:47:55 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3463 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 1.642698 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): -40.81000 16.36300 ymin,ymax (A): -12.06800 49.52300 zmin,zma (A): -51.62200 13.39300 x,y,z range (A): 57.17300 61.59100 65.01500 scale (grids/A): 1.642698 object centre (A): -12.22350 18.72750 -19.11450 number of atom coordinates read : 3463 total number of charged atoms : 3319 net assigned charge : 11.22603 assigned positive charge : 513.7744 centred at (gu) : 88.79797 90.33925 94.81119 assigned negative charge : -502.5501 centred at (gu) : 89.08611 90.10477 95.48401 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 77931 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33498 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 23378 mr = 51839 m= 2386 mr = 15688 m= 57 mr = 1106 m= 1 mr = 3 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 909 time to turn everything in is 0.5600000 number of dielectric boundary points 35118 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 355 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 25416 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) : 0.5475659 object centre at (A) : -12.22350 18.72750 -19.11450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6900800E-02 1.4364527E-03 midg,1,midg; midg,igrid,midg 1.5804652E-02 3.3032913E-02 1,midg,midg; igrid,midg,midg 8.7571600E-03 -3.6192329E-03 gauss-seidel spectral radius is 0.9982763 estimated iterations to convergence 191 setup time was (sec) 0.8700000 now iterating at: 01:47:56 rms-change max change #iterations 3.622739 181.6105 at 10iterations 1.535560 57.75107 at 20iterations 0.6539438 24.42355 at 30iterations 0.2782371 9.196809 at 40iterations 0.1185827 3.631788 at 50iterations 5.0552391E-02 1.707782 at 60iterations 2.1405391E-02 0.7258530 at 70iterations 9.1613876E-03 0.3046341 at 80iterations 3.8914762E-03 0.1381388 at 90iterations 1.6665580E-03 5.8496118E-02 at 100iterations 7.1134075E-04 2.5196075E-02 at 110iterations 3.0318927E-04 1.1165142E-02 at 120iterations finished qdiffx linear iterations at : 01:48:05 total time elapsed so far: 9.800000 # loops : 120 mean,max change (kT/e) : 3.0318927E-04 1.1165142E-02 energy calculations done at 9.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.01000 DelPhi exited at 01:48:05 10.016u 0.261s 0:10.65 96.4% 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 01:48:05 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3463 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.464047 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): -40.81000 16.36300 ymin,ymax (A): -12.06800 49.52300 zmin,zma (A): -51.62200 13.39300 x,y,z range (A): 57.17300 61.59100 65.01500 scale (grids/A): 2.464047 object centre (A): -12.22350 18.72750 -19.11450 number of atom coordinates read : 3463 total number of charged atoms : 3319 net assigned charge : 11.22603 assigned positive charge : 513.7744 centred at (gu) : 88.19665 90.50855 97.21663 assigned negative charge : -502.5501 centred at (gu) : 88.62914 90.15704 98.22607 start vw surface at 0.1800000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 180950 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33498 grid for indexing accessible points = 1.400000 m= 81404 mr = 127484 m= 22888 mr = 63255 m= 3699 mr = 16857 m= 241 mr = 2328 m= 11 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 2962 time to turn everything in is 1.300000 number of dielectric boundary points 79175 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 26499 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) : 1.642698 object centre at (A) : -12.22350 18.72750 -19.11450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4356540 2.6687237E-02 midg,1,midg; midg,igrid,midg 0.3607027 0.5716293 1,midg,midg; igrid,midg,midg 0.1374091 -2.5549466E-02 gauss-seidel spectral radius is 0.9991873 estimated iterations to convergence 277 setup time was (sec) 1.590000 now iterating at: 01:48:07 rms-change max change #iterations 9.520082 342.9323 at 10iterations 5.486035 137.6106 at 20iterations 3.140243 84.01427 at 30iterations 1.784675 44.19648 at 40iterations 1.010767 24.39445 at 50iterations 0.5703089 14.71623 at 60iterations 0.3209394 6.399805 at 70iterations 0.1805871 3.548077 at 80iterations 0.1013786 2.058025 at 90iterations 5.6828633E-02 1.210905 at 100iterations 3.1847086E-02 0.7900257 at 110iterations 1.7816259E-02 0.3556213 at 120iterations 9.9869249E-03 0.2027397 at 130iterations 5.5891033E-03 0.1180840 at 140iterations 3.1204741E-03 5.8571815E-02 at 150iterations 1.7454955E-03 3.1357765E-02 at 160iterations 9.7634923E-04 1.8346310E-02 at 170iterations 5.4639974E-04 1.0787964E-02 at 180iterations finished qdiffx linear iterations at : 01:48:17 total time elapsed so far: 11.94000 # loops : 180 mean,max change (kT/e) : 5.4639974E-04 1.0787964E-02 energy calculations done at 11.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.14000 DelPhi exited at 01:48:18 12.138u 0.210s 0:12.67 97.3% 0+0k 0+0io 0pf+0w