Sun Oct 9 15:00:51 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 15:00:51 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1874 !!! WARNING: HIR 87 has a net charge of 0.5140 !!! WARNING: GLU 107 has a net charge of -2.0000 !!! WARNING: GLU 321 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6534748 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): -4.706000 43.95600 ymin,ymax (A): -11.79800 42.68000 zmin,zma (A): -5.667000 35.44500 x,y,z range (A): 48.66200 54.47800 41.11200 scale (grids/A): 0.6534748 object centre (A): 19.62500 15.44100 14.88900 number of atom coordinates read : 1874 total number of charged atoms : 1742 net assigned charge : 2.014009 assigned positive charge : 287.3910 centred at (gu) : 88.77674 89.97975 91.52186 assigned negative charge : -285.3771 centred at (gu) : 88.78426 89.91769 91.41417 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5506 nv = 96 ne = 84 npr = 35844 no. pairs analyzed = 35844 no. exposed pairs = 2780 no. arc points = 20084 no. surface atoms = 910 nbur = 964 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 304 mr = 2540 m= 3 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 6.9999993E-02 no. cavity mid-points inaccessible to solvent = 48 time to turn everything in is 0.1600000 number of dielectric boundary points 3253 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1839 ## 168 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6257 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.6745236E-09 2.3625903E-08 midg,1,midg; midg,igrid,midg -3.6250394E-09 1.1541882E-08 1,midg,midg; igrid,midg,midg 6.3800165E-09 2.4532716E-09 gauss-seidel spectral radius is 0.9878110 estimated iterations to convergence 74 setup time was (sec) 0.3500000 now iterating at: 15:00:51 rms-change max change #iterations 0.1348001 21.88161 at 10iterations 1.4047069E-02 2.510481 at 20iterations 1.4202229E-03 0.2714539 at 30iterations 1.5359768E-04 2.3153305E-02 at 40iterations 1.9620475E-05 2.7008057E-03 at 50iterations finished qdiffx linear iterations at : 15:00:54 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.9620475E-05 2.7008057E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 15:00:55 3.358u 0.166s 0:03.78 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 Sun Oct 9 2011 at 15:00:55 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1874 !!! WARNING: HIR 87 has a net charge of 0.5140 !!! WARNING: GLU 107 has a net charge of -2.0000 !!! WARNING: GLU 321 has a net charge of -2.0000 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: 1.960424 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): -4.706000 43.95600 ymin,ymax (A): -11.79800 42.68000 zmin,zma (A): -5.667000 35.44500 x,y,z range (A): 48.66200 54.47800 41.11200 scale (grids/A): 1.960424 object centre (A): 19.62500 15.44100 14.88900 number of atom coordinates read : 1874 total number of charged atoms : 1742 net assigned charge : 2.014009 assigned positive charge : 287.3910 centred at (gu) : 86.33056 89.93954 94.56531 assigned negative charge : -285.3771 centred at (gu) : 86.35286 89.75329 94.24252 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 58428 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20084 grid for indexing accessible points = 1.400000 m= 19302 mr = 36470 m= 2953 mr = 12832 m= 192 mr = 1539 m= 4 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 390 time to turn everything in is 0.3100000 number of dielectric boundary points 29962 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 13766 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) : 0.6534748 object centre at (A) : 19.62500 15.44100 14.88900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.5402111E-04 1.4449583E-02 midg,1,midg; midg,igrid,midg -2.9869715E-02 -1.6373208E-02 1,midg,midg; igrid,midg,midg 2.7723918E-02 1.0915801E-02 gauss-seidel spectral radius is 0.9986562 estimated iterations to convergence 216 setup time was (sec) 0.5100000 now iterating at: 15:00:56 rms-change max change #iterations 3.827186 157.2875 at 10iterations 1.799580 69.11739 at 20iterations 0.8466205 30.86764 at 30iterations 0.3975300 13.96761 at 40iterations 0.1875229 6.431326 at 50iterations 8.7623671E-02 3.032482 at 60iterations 4.1245267E-02 1.552666 at 70iterations 1.9252289E-02 0.6209497 at 80iterations 9.0863947E-03 0.3236542 at 90iterations 4.2614476E-03 0.1429234 at 100iterations 2.0099073E-03 7.5876236E-02 at 110iterations 9.4544352E-04 3.2697678E-02 at 120iterations finished qdiffx linear iterations at : 15:01:03 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 9.4544352E-04 3.2697678E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 15:01:03 7.700u 0.199s 0:08.15 96.8% 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 Sun Oct 9 2011 at 15:01:03 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1874 !!! WARNING: HIR 87 has a net charge of 0.5140 !!! WARNING: GLU 107 has a net charge of -2.0000 !!! WARNING: GLU 321 has a net charge of -2.0000 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: 2.940637 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): -4.706000 43.95600 ymin,ymax (A): -11.79800 42.68000 zmin,zma (A): -5.667000 35.44500 x,y,z range (A): 48.66200 54.47800 41.11200 scale (grids/A): 2.940637 object centre (A): 19.62500 15.44100 14.88900 number of atom coordinates read : 1874 total number of charged atoms : 1742 net assigned charge : 2.014009 assigned positive charge : 287.3910 centred at (gu) : 84.49588 89.90931 96.84807 assigned negative charge : -285.3771 centred at (gu) : 84.52926 89.62997 96.36378 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 134871 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20084 grid for indexing accessible points = 1.400000 m= 62603 mr = 89458 m= 21298 mr = 47827 m= 5068 mr = 15841 m= 744 mr = 3406 m= 64 mr = 453 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 1329 time to turn everything in is 0.7500000 number of dielectric boundary points 67636 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 13935 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) : 1.960424 object centre at (A) : 19.62500 15.44100 14.88900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5073938E-02 0.1202181 midg,1,midg; midg,igrid,midg -0.2928102 -0.2531691 1,midg,midg; igrid,midg,midg 0.3366336 0.1076308 gauss-seidel spectral radius is 0.9992769 estimated iterations to convergence 293 setup time was (sec) 0.9800000 now iterating at: 15:01:04 rms-change max change #iterations 9.346333 434.8125 at 10iterations 5.659915 215.2980 at 20iterations 3.404038 90.83731 at 30iterations 2.031296 49.25365 at 40iterations 1.203960 27.30896 at 50iterations 0.7110783 17.61575 at 60iterations 0.4184152 9.599520 at 70iterations 0.2458019 6.276123 at 80iterations 0.1434925 3.155008 at 90iterations 8.3675303E-02 1.854527 at 100iterations 4.8835710E-02 0.9955893 at 110iterations 2.8428018E-02 0.6521683 at 120iterations 1.6515790E-02 0.3388138 at 130iterations 9.5986128E-03 0.1998901 at 140iterations 5.5759968E-03 0.1287365 at 150iterations 3.2339669E-03 6.3262939E-02 at 160iterations 1.8754540E-03 3.7235260E-02 at 170iterations 1.0881325E-03 2.4343491E-02 at 180iterations finished qdiffx linear iterations at : 15:01:15 total time elapsed so far: 12.28000 # loops : 180 mean,max change (kT/e) : 1.0881325E-03 2.4343491E-02 energy calculations done at 12.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.41000 DelPhi exited at 15:01:16 12.416u 0.203s 0:12.87 97.9% 0+0k 0+0io 0pf+0w