Sun Oct 9 14:06:04 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 14:06:04 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2355 !!! WARNING: GLM 182 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6993968 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): -13.75300 35.65100 ymin,ymax (A): -0.6240000 50.27700 zmin,zma (A): 1.587000 44.84900 x,y,z range (A): 49.40400 50.90100 43.26200 scale (grids/A): 0.6993968 object centre (A): 10.94900 24.82650 23.21800 number of atom coordinates read : 2355 total number of charged atoms : 2210 net assigned charge : 3.406020 assigned positive charge : 361.2711 centred at (gu) : 89.50526 88.71612 90.79330 assigned negative charge : -357.8656 centred at (gu) : 89.47935 88.52849 90.86253 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7812 nv = 96 ne = 84 npr = 47200 no. pairs analyzed = 47200 no. exposed pairs = 2934 no. arc points = 20375 no. surface atoms = 990 nbur = 1365 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 506 mr = 4413 m= 2 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 1 time to turn everything in is 0.2000000 number of dielectric boundary points 3827 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1868 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8772 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9500166E-08 -9.0583843E-09 midg,1,midg; midg,igrid,midg -8.4635779E-08 8.7093795E-08 1,midg,midg; igrid,midg,midg 1.4374014E-08 3.4149192E-08 gauss-seidel spectral radius is 0.9893754 estimated iterations to convergence 79 setup time was (sec) 0.3900000 now iterating at: 14:06:04 rms-change max change #iterations 0.2057115 30.55362 at 10iterations 2.5512155E-02 3.392874 at 20iterations 3.5862213E-03 0.4998140 at 30iterations 7.8110956E-04 0.1309528 at 40iterations 2.4897431E-04 4.1572571E-02 at 50iterations finished qdiffx linear iterations at : 14:06:07 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 2.4897431E-04 4.1572571E-02 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 14:06:08 3.393u 0.167s 0:03.83 92.6% 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 14:06:08 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2355 !!! WARNING: GLM 182 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.098191 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): -13.75300 35.65100 ymin,ymax (A): -0.6240000 50.27700 zmin,zma (A): 1.587000 44.84900 x,y,z range (A): 49.40400 50.90100 43.26200 scale (grids/A): 2.098191 object centre (A): 10.94900 24.82650 23.21800 number of atom coordinates read : 2355 total number of charged atoms : 2210 net assigned charge : 3.406020 assigned positive charge : 361.2711 centred at (gu) : 88.51550 86.14784 92.37948 assigned negative charge : -357.8656 centred at (gu) : 88.43788 85.58533 92.58734 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 82877 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20375 grid for indexing accessible points = 1.400000 m= 32841 mr = 58052 m= 6102 mr = 24667 m= 539 mr = 3972 m= 12 mr = 255 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.4300000 number of dielectric boundary points 35425 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 77 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 17533 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) : 0.6993968 object centre at (A) : 10.94900 24.82650 23.21800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1044125E-02 9.4473769E-04 midg,1,midg; midg,igrid,midg -5.2534658E-02 1.4772560E-02 1,midg,midg; igrid,midg,midg -1.6988186E-02 5.4803487E-02 gauss-seidel spectral radius is 0.9988400 estimated iterations to convergence 232 setup time was (sec) 0.6400000 now iterating at: 14:06:09 rms-change max change #iterations 4.918623 215.9470 at 10iterations 2.439025 81.82039 at 20iterations 1.206463 38.55824 at 30iterations 0.5991381 20.56805 at 40iterations 0.2985805 9.219122 at 50iterations 0.1483332 4.441107 at 60iterations 7.4128687E-02 2.104717 at 70iterations 3.6940958E-02 1.023841 at 80iterations 1.8636744E-02 0.5908070 at 90iterations 9.4355810E-03 0.2625370 at 100iterations 4.8683048E-03 0.1497192 at 110iterations 2.6088895E-03 8.4571838E-02 at 120iterations finished qdiffx linear iterations at : 14:06:16 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 2.6088895E-03 8.4571838E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 14:06:16 7.902u 0.185s 0:08.35 96.7% 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 14:06:16 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2355 !!! WARNING: GLM 182 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.147286 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): -13.75300 35.65100 ymin,ymax (A): -0.6240000 50.27700 zmin,zma (A): 1.587000 44.84900 x,y,z range (A): 49.40400 50.90100 43.26200 scale (grids/A): 3.147286 object centre (A): 10.94900 24.82650 23.21800 number of atom coordinates read : 2355 total number of charged atoms : 2210 net assigned charge : 3.406020 assigned positive charge : 361.2711 centred at (gu) : 87.77331 84.22163 93.56912 assigned negative charge : -357.8656 centred at (gu) : 87.65669 83.37798 93.88087 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 191155 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20375 grid for indexing accessible points = 1.400000 m= 101925 mr = 139955 m= 40967 mr = 84274 m= 11441 mr = 33357 m= 2167 mr = 8688 m= 199 mr = 1563 m= 5 mr = 90 m= 0 mr = 2 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 113 time to turn everything in is 1.260000 number of dielectric boundary points 79930 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 17672 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) : 2.098191 object centre at (A) : 10.94900 24.82650 23.21800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4991293 -0.1005635 midg,1,midg; midg,igrid,midg -0.5564023 0.2765392 1,midg,midg; igrid,midg,midg -0.6063032 0.5117833 gauss-seidel spectral radius is 0.9993030 estimated iterations to convergence 299 setup time was (sec) 1.500000 now iterating at: 14:06:18 rms-change max change #iterations 11.13567 361.0479 at 10iterations 6.668284 170.9963 at 20iterations 3.990135 75.67611 at 30iterations 2.363891 45.45511 at 40iterations 1.404146 23.73519 at 50iterations 0.8281484 12.93165 at 60iterations 0.4899797 8.599775 at 70iterations 0.2890728 5.132736 at 80iterations 0.1698135 2.875751 at 90iterations 0.1001737 1.732182 at 100iterations 5.8917284E-02 1.073586 at 110iterations 3.4822144E-02 0.6291301 at 120iterations 2.0736683E-02 0.3628349 at 130iterations 1.2507009E-02 0.2291708 at 140iterations 7.7682137E-03 0.1439590 at 150iterations 5.0243307E-03 0.1085510 at 160iterations 3.4444528E-03 7.6446533E-02 at 170iterations 2.5174317E-03 5.5526733E-02 at 180iterations finished qdiffx linear iterations at : 14:06:29 total time elapsed so far: 12.95000 # loops : 180 mean,max change (kT/e) : 2.5174317E-03 5.5526733E-02 energy calculations done at 12.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.08000 DelPhi exited at 14:06:30 13.087u 0.214s 0:13.56 98.0% 0+0k 0+0io 0pf+0w