Sat Oct 8 15:21:46 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 Sat Oct 8 2011 at 15:21:46 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3253 !!! WARNING: GLM 117 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6097874 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): -61.01500 -2.634000 ymin,ymax (A): -26.39200 25.85300 zmin,zma (A): -10.30300 45.09400 x,y,z range (A): 58.38100 52.24500 55.39700 scale (grids/A): 0.6097874 object centre (A): -31.82450 -0.2694998 17.39550 number of atom coordinates read : 3253 total number of charged atoms : 3104 net assigned charge : 5.406016 assigned positive charge : 486.6387 centred at (gu) : 91.66257 89.24712 90.79381 assigned negative charge : -481.2341 centred at (gu) : 91.70287 89.27840 90.79628 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7944 nv = 96 ne = 84 npr = 67354 no. pairs analyzed = 67354 no. exposed pairs = 3660 no. arc points = 25800 no. surface atoms = 1239 nbur = 2014 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 370 mr = 4560 m= 0 mr = 36 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3718 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2639 ## 273 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 9992 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8121439E-09 3.6069960E-09 midg,1,midg; midg,igrid,midg 6.0021010E-09 1.1038087E-09 1,midg,midg; igrid,midg,midg 3.9065413E-09 9.7679886E-10 gauss-seidel spectral radius is 0.9861263 estimated iterations to convergence 70 setup time was (sec) 0.6900000 now iterating at: 15:21:47 rms-change max change #iterations 0.1297011 15.53901 at 10iterations 1.2059928E-02 1.639299 at 20iterations 1.0784727E-03 0.1532478 at 30iterations 1.0072404E-04 1.2920380E-02 at 40iterations 1.0595147E-05 1.3732910E-03 at 50iterations finished qdiffx linear iterations at : 15:21:50 total time elapsed so far: 4.090000 # loops : 50 mean,max change (kT/e) : 1.0595147E-05 1.3732910E-03 energy calculations done at 4.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.270000 DelPhi exited at 15:21:51 4.277u 0.291s 0:04.91 92.8% 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 Sat Oct 8 2011 at 15:21:51 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3253 !!! WARNING: GLM 117 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.829362 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): -61.01500 -2.634000 ymin,ymax (A): -26.39200 25.85300 zmin,zma (A): -10.30300 45.09400 x,y,z range (A): 58.38100 52.24500 55.39700 scale (grids/A): 1.829362 object centre (A): -31.82450 -0.2694998 17.39550 number of atom coordinates read : 3253 total number of charged atoms : 3104 net assigned charge : 5.406016 assigned positive charge : 486.6387 centred at (gu) : 94.98694 87.74049 92.38058 assigned negative charge : -481.2341 centred at (gu) : 95.10848 87.83485 92.38853 start vw surface at 0.1600000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 87800 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25800 grid for indexing accessible points = 1.400000 m= 30562 mr = 63265 m= 4035 mr = 22701 m= 157 mr = 2388 m= 0 mr = 27 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 2356 time to turn everything in is 0.7400000 number of dielectric boundary points 34173 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 209 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 24281 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) : 0.6097874 object centre at (A) : -31.82450 -0.2694998 17.39550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.3030195E-03 -1.7554220E-02 midg,1,midg; midg,igrid,midg 1.7580908E-02 1.0031025E-02 1,midg,midg; igrid,midg,midg 3.6675915E-02 1.7425677E-02 gauss-seidel spectral radius is 0.9985790 estimated iterations to convergence 210 setup time was (sec) 1.060000 now iterating at: 15:21:52 rms-change max change #iterations 4.429815 168.6578 at 10iterations 2.038882 66.31898 at 20iterations 0.9438072 28.73099 at 30iterations 0.4355040 13.23761 at 40iterations 0.2010902 5.980930 at 50iterations 9.2901275E-02 2.821838 at 60iterations 4.2965468E-02 1.168839 at 70iterations 1.9768691E-02 0.5710509 at 80iterations 9.1584148E-03 0.2889166 at 90iterations 4.2415177E-03 0.1299477 at 100iterations 1.9538333E-03 5.6800246E-02 at 110iterations 9.0147310E-04 2.7496338E-02 at 120iterations finished qdiffx linear iterations at : 15:22:01 total time elapsed so far: 9.810000 # loops : 120 mean,max change (kT/e) : 9.0147310E-04 2.7496338E-02 energy calculations done at 9.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.980000 DelPhi exited at 15:22:01 9.982u 0.349s 0:10.61 97.2% 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 Sat Oct 8 2011 at 15:22:02 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3253 !!! WARNING: GLM 117 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.744043 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): -61.01500 -2.634000 ymin,ymax (A): -26.39200 25.85300 zmin,zma (A): -10.30300 45.09400 x,y,z range (A): 58.38100 52.24500 55.39700 scale (grids/A): 2.744043 object centre (A): -31.82450 -0.2694998 17.39550 number of atom coordinates read : 3253 total number of charged atoms : 3104 net assigned charge : 5.406016 assigned positive charge : 486.6387 centred at (gu) : 97.48011 86.61053 93.57066 assigned negative charge : -481.2341 centred at (gu) : 97.66257 86.75216 93.58271 start vw surface at 0.1800000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 203605 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25800 grid for indexing accessible points = 1.400000 m= 102501 mr = 153222 m= 33762 mr = 84790 m= 6823 mr = 26886 m= 673 mr = 5047 m= 15 mr = 378 m= 0 mr = 2 time to grow re-entrant surface = 1.160000 no. cavity mid-points inaccessible to solvent = 8092 time to turn everything in is 1.940000 number of dielectric boundary points 77054 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 2.090000 number of grid points assigned charge 24830 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) : 1.829362 object centre at (A) : -31.82450 -0.2694998 17.39550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2640647E-02 -0.1554195 midg,1,midg; midg,igrid,midg 7.4036434E-02 0.1192751 1,midg,midg; igrid,midg,midg 0.4671255 0.1961527 gauss-seidel spectral radius is 0.9992512 estimated iterations to convergence 288 setup time was (sec) 2.280000 now iterating at: 15:22:04 rms-change max change #iterations 10.44638 345.6815 at 10iterations 6.024179 113.0354 at 20iterations 3.462919 60.92121 at 30iterations 1.985952 35.31528 at 40iterations 1.139995 20.14412 at 50iterations 0.6526830 11.65939 at 60iterations 0.3745423 6.624989 at 70iterations 0.2144191 4.213181 at 80iterations 0.1225113 2.381905 at 90iterations 7.0379183E-02 1.170990 at 100iterations 4.0198542E-02 0.7073412 at 110iterations 2.3040570E-02 0.4105396 at 120iterations 1.3173584E-02 0.2222862 at 130iterations 7.5593679E-03 0.1413336 at 140iterations 4.3239603E-03 7.2863579E-02 at 150iterations 2.4783453E-03 4.1837692E-02 at 160iterations 1.4254855E-03 2.5321960E-02 at 170iterations 8.1692805E-04 1.3710022E-02 at 180iterations finished qdiffx linear iterations at : 15:22:19 total time elapsed so far: 16.91000 # loops : 180 mean,max change (kT/e) : 8.1692805E-04 1.3710022E-02 energy calculations done at 16.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.10000 DelPhi exited at 15:22:19 17.098u 0.364s 0:17.74 98.3% 0+0k 0+0io 0pf+0w