Tue Oct 11 05:28:44 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 Tue Oct 11 2011 at 05:28:44 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 = 2246 !!! WARNING: HIR 40 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6926475 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): 19.81500 63.11300 ymin,ymax (A): -3.596000 34.76300 zmin,zma (A): 20.49100 71.88800 x,y,z range (A): 43.29800 38.35900 51.39700 scale (grids/A): 0.6926475 object centre (A): 41.46400 15.58350 46.18950 number of atom coordinates read : 2246 total number of charged atoms : 1929 net assigned charge : 7.514009 assigned positive charge : 313.2890 centred at (gu) : 90.14103 89.33284 89.29639 assigned negative charge : -305.7751 centred at (gu) : 90.32468 89.35038 89.28761 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6766 nv = 96 ne = 84 npr = 40994 no. pairs analyzed = 40994 no. exposed pairs = 2506 no. arc points = 17107 no. surface atoms = 852 nbur = 1394 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 448 mr = 3913 m= 6 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3247 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1613 ## 118 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7479 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7421377E-08 4.1524732E-08 midg,1,midg; midg,igrid,midg 5.7515027E-08 3.3854619E-08 1,midg,midg; igrid,midg,midg 1.0386609E-07 -2.0888907E-08 gauss-seidel spectral radius is 0.9891382 estimated iterations to convergence 78 setup time was (sec) 0.5200000 now iterating at: 05:28:45 rms-change max change #iterations 0.1754844 24.04939 at 10iterations 2.0964732E-02 2.967692 at 20iterations 2.6699875E-03 0.4207268 at 30iterations 4.5924092E-04 5.7789803E-02 at 40iterations 1.1975167E-04 1.3860703E-02 at 50iterations finished qdiffx linear iterations at : 05:28:48 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 1.1975167E-04 1.3860703E-02 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 05:28:48 3.331u 0.141s 0:03.79 91.5% 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 Tue Oct 11 2011 at 05:28:48 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 = 2246 !!! WARNING: HIR 40 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.077942 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): 19.81500 63.11300 ymin,ymax (A): -3.596000 34.76300 zmin,zma (A): 20.49100 71.88800 x,y,z range (A): 43.29800 38.35900 51.39700 scale (grids/A): 2.077942 object centre (A): 41.46400 15.58350 46.18950 number of atom coordinates read : 2246 total number of charged atoms : 1929 net assigned charge : 7.514009 assigned positive charge : 313.2890 centred at (gu) : 90.42307 87.99863 87.88917 assigned negative charge : -305.7751 centred at (gu) : 90.97411 88.05128 87.86282 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 72103 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17107 grid for indexing accessible points = 1.400000 m= 29059 mr = 51322 m= 5555 mr = 22159 m= 491 mr = 3740 m= 10 mr = 253 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 29744 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 15301 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) : 0.6926475 object centre at (A) : 41.46400 15.58350 46.18950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2996781E-02 3.8031265E-02 midg,1,midg; midg,igrid,midg 2.6725274E-02 1.2800585E-02 1,midg,midg; igrid,midg,midg 4.0624019E-02 1.0570196E-02 gauss-seidel spectral radius is 0.9987857 estimated iterations to convergence 227 setup time was (sec) 0.8500000 now iterating at: 05:28:49 rms-change max change #iterations 4.401465 208.0555 at 10iterations 2.163681 65.14415 at 20iterations 1.055173 35.22300 at 30iterations 0.5200554 16.81057 at 40iterations 0.2546150 7.633072 at 50iterations 0.1247435 3.929224 at 60iterations 6.1177094E-02 1.869859 at 70iterations 3.0057661E-02 0.9610476 at 80iterations 1.4785639E-02 0.4381924 at 90iterations 7.2840666E-03 0.2293873 at 100iterations 3.6140264E-03 0.1108279 at 110iterations 1.8233180E-03 5.6902647E-02 at 120iterations finished qdiffx linear iterations at : 05:28:56 total time elapsed so far: 7.350000 # loops : 120 mean,max change (kT/e) : 1.8233180E-03 5.6902647E-02 energy calculations done at 7.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.530000 DelPhi exited at 05:28:56 7.536u 0.154s 0:07.96 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 Tue Oct 11 2011 at 05:28:56 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 = 2246 !!! WARNING: HIR 40 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.116914 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): 19.81500 63.11300 ymin,ymax (A): -3.596000 34.76300 zmin,zma (A): 20.49100 71.88800 x,y,z range (A): 43.29800 38.35900 51.39700 scale (grids/A): 3.116914 object centre (A): 41.46400 15.58350 46.18950 number of atom coordinates read : 2246 total number of charged atoms : 1929 net assigned charge : 7.514009 assigned positive charge : 313.2890 centred at (gu) : 90.63456 86.99802 86.83366 assigned negative charge : -305.7751 centred at (gu) : 91.46117 87.07696 86.79426 start vw surface at 0.1500000 fill in re-entrant regions at 0.7900000 boundary points on vw surface= 166110 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17107 grid for indexing accessible points = 1.400000 m= 90926 mr = 123516 m= 36714 mr = 75713 m= 10512 mr = 30309 m= 2002 mr = 8223 m= 232 mr = 1520 m= 5 mr = 158 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.770000 number of dielectric boundary points 67062 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 15432 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) : 2.077942 object centre at (A) : 41.46400 15.58350 46.18950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4314032 0.2858365 midg,1,midg; midg,igrid,midg 0.2237373 0.1083312 1,midg,midg; igrid,midg,midg 0.3252074 0.2581081 gauss-seidel spectral radius is 0.9992827 estimated iterations to convergence 295 setup time was (sec) 2.070000 now iterating at: 05:28:59 rms-change max change #iterations 9.960754 427.6154 at 10iterations 5.879794 150.7409 at 20iterations 3.456312 74.85016 at 30iterations 2.028305 39.13988 at 40iterations 1.187249 22.72369 at 50iterations 0.6938303 13.17790 at 60iterations 0.4046012 7.242545 at 70iterations 0.2369364 4.669128 at 80iterations 0.1378769 2.550411 at 90iterations 8.0338232E-02 1.446471 at 100iterations 4.6938304E-02 0.8730221 at 110iterations 2.7427237E-02 0.5964527 at 120iterations 1.6087381E-02 0.2820797 at 130iterations 9.5435763E-03 0.1844292 at 140iterations 5.7406272E-03 0.1093960 at 150iterations 3.5385811E-03 6.6596985E-02 at 160iterations 2.2825210E-03 4.3607712E-02 at 170iterations 1.5524250E-03 2.6191711E-02 at 180iterations finished qdiffx linear iterations at : 05:29:09 total time elapsed so far: 12.18000 # loops : 180 mean,max change (kT/e) : 1.5524250E-03 2.6191711E-02 energy calculations done at 12.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.37000 DelPhi exited at 05:29:09 12.377u 0.167s 0:13.11 95.5% 0+0k 0+0io 0pf+0w