Mon Oct 10 19:34:02 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 Mon Oct 10 2011 at 19:34:02 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3117 !!! WARNING: HIT 99 has a net charge of 0.5140 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: 0.5542236 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): -31.93600 32.29800 ymin,ymax (A): -23.93600 25.82100 zmin,zma (A): 19.50600 76.50600 x,y,z range (A): 64.23400 49.75700 57.00000 scale (grids/A): 0.5542236 object centre (A): 0.1809998 0.9425011 48.00600 number of atom coordinates read : 3117 total number of charged atoms : 2976 net assigned charge : 3.514023 assigned positive charge : 475.3966 centred at (gu) : 90.95689 90.28528 87.99710 assigned negative charge : -471.8839 centred at (gu) : 90.88112 90.42924 88.05685 start vw surface at 0.1600000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6398 nv = 96 ne = 84 npr = 59553 no. pairs analyzed = 59553 no. exposed pairs = 4448 no. arc points = 32445 no. surface atoms = 1483 nbur = 1634 mkacc time = 0.2000000 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 = 1.568000 m= 237 mr = 2936 m= 0 mr = 9 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 3690 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3254 ## 423 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 8290 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3916045E-09 -1.7173934E-10 midg,1,midg; midg,igrid,midg 1.5182750E-09 -1.1915015E-09 1,midg,midg; igrid,midg,midg -3.4679942E-10 1.2629298E-09 gauss-seidel spectral radius is 0.9832366 estimated iterations to convergence 64 setup time was (sec) 0.7800000 now iterating at: 19:34:03 rms-change max change #iterations 7.9762787E-02 14.37659 at 10iterations 5.7704095E-03 0.9004784 at 20iterations 5.2098214E-04 9.4657898E-02 at 30iterations 8.7656488E-05 2.2003174E-02 at 40iterations 2.0158761E-05 5.3005219E-03 at 50iterations finished qdiffx linear iterations at : 19:34:07 total time elapsed so far: 4.640000 # loops : 50 mean,max change (kT/e) : 2.0158761E-05 5.3005219E-03 energy calculations done at 4.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.860000 DelPhi exited at 19:34:08 4.868u 0.466s 0:05.76 92.3% 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 Mon Oct 10 2011 at 19:34:08 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3117 !!! WARNING: HIT 99 has a net charge of 0.5140 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: 1.662671 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): -31.93600 32.29800 ymin,ymax (A): -23.93600 25.82100 zmin,zma (A): 19.50600 76.50600 x,y,z range (A): 64.23400 49.75700 57.00000 scale (grids/A): 1.662671 object centre (A): 0.1809998 0.9425011 48.00600 number of atom coordinates read : 3117 total number of charged atoms : 2976 net assigned charge : 3.514023 assigned positive charge : 475.3966 centred at (gu) : 92.86966 90.85488 83.99030 assigned negative charge : -471.8839 centred at (gu) : 92.64301 91.28723 84.17004 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 70172 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32445 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 20496 mr = 44628 m= 2025 mr = 13114 m= 55 mr = 858 m= 0 mr = 2 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 156 time to turn everything in is 0.7200000 number of dielectric boundary points 34146 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 339 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 22874 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) : 0.5542236 object centre at (A) : 0.1809998 0.9425011 48.00600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3047354E-02 6.0223104E-03 midg,1,midg; midg,igrid,midg 4.9972697E-03 -1.7896075E-02 1,midg,midg; igrid,midg,midg -1.6578389E-02 2.8733771E-02 gauss-seidel spectral radius is 0.9982908 estimated iterations to convergence 192 setup time was (sec) 1.060000 now iterating at: 19:34:09 rms-change max change #iterations 3.605217 146.5426 at 10iterations 1.533539 62.95654 at 20iterations 0.6515375 26.23376 at 30iterations 0.2780566 10.50139 at 40iterations 0.1187864 3.934394 at 50iterations 5.0803401E-02 2.066653 at 60iterations 2.1711137E-02 0.8152198 at 70iterations 9.2941215E-03 0.3399467 at 80iterations 3.9945533E-03 0.1371739 at 90iterations 1.7247214E-03 6.1950684E-02 at 100iterations 7.5049425E-04 2.7587891E-02 at 110iterations 3.3247247E-04 1.2664795E-02 at 120iterations finished qdiffx linear iterations at : 19:34:19 total time elapsed so far: 10.69000 # loops : 120 mean,max change (kT/e) : 3.3247247E-04 1.2664795E-02 energy calculations done at 10.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.91000 DelPhi exited at 19:34:20 10.913u 0.501s 0:12.09 94.3% 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 Mon Oct 10 2011 at 19:34:20 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3117 !!! WARNING: HIT 99 has a net charge of 0.5140 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: 2.494006 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): -31.93600 32.29800 ymin,ymax (A): -23.93600 25.82100 zmin,zma (A): 19.50600 76.50600 x,y,z range (A): 64.23400 49.75700 57.00000 scale (grids/A): 2.494006 object centre (A): 0.1809998 0.9425011 48.00600 number of atom coordinates read : 3117 total number of charged atoms : 2976 net assigned charge : 3.514023 assigned positive charge : 475.3966 centred at (gu) : 94.30416 91.28210 80.98530 assigned negative charge : -471.8839 centred at (gu) : 93.96439 91.93065 81.25500 start vw surface at 0.1700000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 162833 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32445 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 70882 mr = 109766 m= 19386 mr = 53793 m= 3100 mr = 13775 m= 241 mr = 1848 m= 2 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 580 time to turn everything in is 1.770000 number of dielectric boundary points 77159 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 23794 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) : 1.662671 object centre at (A) : 0.1809998 0.9425011 48.00600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1652353 9.2229478E-02 midg,1,midg; midg,igrid,midg 5.0880592E-02 -0.2265244 1,midg,midg; igrid,midg,midg -0.1330733 0.6014591 gauss-seidel spectral radius is 0.9991896 estimated iterations to convergence 277 setup time was (sec) 2.150000 now iterating at: 19:34:23 rms-change max change #iterations 9.279683 298.2216 at 10iterations 5.284674 128.4454 at 20iterations 2.999777 75.68622 at 30iterations 1.697277 38.19285 at 40iterations 0.9544782 20.98918 at 50iterations 0.5367218 13.00407 at 60iterations 0.3023032 7.435318 at 70iterations 0.1689885 3.813845 at 80iterations 9.4572313E-02 2.116913 at 90iterations 5.3012341E-02 1.201666 at 100iterations 2.9621823E-02 0.5842667 at 110iterations 1.6624898E-02 0.3453522 at 120iterations 9.2820181E-03 0.1878228 at 130iterations 5.2005355E-03 0.1029396 at 140iterations 2.9099947E-03 5.6488037E-02 at 150iterations 1.6346974E-03 3.3927917E-02 at 160iterations 9.1852568E-04 1.8747330E-02 at 170iterations 5.2062998E-04 1.0494232E-02 at 180iterations finished qdiffx linear iterations at : 19:34:39 total time elapsed so far: 18.23000 # loops : 180 mean,max change (kT/e) : 5.2062998E-04 1.0494232E-02 energy calculations done at 18.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.44000 DelPhi exited at 19:34:40 18.440u 0.514s 0:19.64 96.4% 0+0k 0+0io 0pf+0w