Tue Oct 11 06:56:44 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 06:56:44 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3059 !!! WARNING: UMP 317 has a net charge of -0.1000 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: 0.5794648 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): -17.85600 43.58000 ymin,ymax (A): 19.10800 77.56000 zmin,zma (A): -70.41200 -19.94800 x,y,z range (A): 61.43600 58.45200 50.46400 scale (grids/A): 0.5794648 object centre (A): 12.86200 48.33400 -45.18000 number of atom coordinates read : 3059 total number of charged atoms : 2915 net assigned charge : -5.099980 assigned positive charge : 448.3334 centred at (gu) : 90.05044 89.89677 89.86408 assigned negative charge : -453.4339 centred at (gu) : 90.03304 90.13980 89.84850 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6704 nv = 96 ne = 84 npr = 64403 no. pairs analyzed = 64403 no. exposed pairs = 3786 no. arc points = 26760 no. surface atoms = 1285 nbur = 1774 mkacc time = 0.1700000 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 = 1.484000 m= 349 mr = 3588 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3425 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2687 ## 287 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8561 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4835378E-09 -7.2766876E-10 midg,1,midg; midg,igrid,midg 4.2247570E-09 -6.4587611E-09 1,midg,midg; igrid,midg,midg -1.4612846E-09 -7.1769579E-10 gauss-seidel spectral radius is 0.9846361 estimated iterations to convergence 66 setup time was (sec) 0.6700000 now iterating at: 06:56:45 rms-change max change #iterations 0.1001958 15.85974 at 10iterations 7.8491652E-03 1.114910 at 20iterations 6.4313482E-04 0.1007099 at 30iterations 7.7697936E-05 1.6674995E-02 at 40iterations 1.7780534E-05 3.9234161E-03 at 50iterations finished qdiffx linear iterations at : 06:56:50 total time elapsed so far: 4.870000 # loops : 50 mean,max change (kT/e) : 1.7780534E-05 3.9234161E-03 energy calculations done at 4.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.050000 DelPhi exited at 06:56:50 5.054u 0.432s 0:05.79 94.6% 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 Tue Oct 11 2011 at 06:56:50 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3059 !!! WARNING: UMP 317 has a net charge of -0.1000 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: 1.738394 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): -17.85600 43.58000 ymin,ymax (A): 19.10800 77.56000 zmin,zma (A): -70.41200 -19.94800 x,y,z range (A): 61.43600 58.45200 50.46400 scale (grids/A): 1.738394 object centre (A): 12.86200 48.33400 -45.18000 number of atom coordinates read : 3059 total number of charged atoms : 2915 net assigned charge : -5.099980 assigned positive charge : 448.3334 centred at (gu) : 90.15067 89.68961 89.59169 assigned negative charge : -453.4339 centred at (gu) : 90.09862 90.41924 89.54496 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 72107 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26760 grid for indexing accessible points = 1.400000 m= 25994 mr = 49190 m= 3905 mr = 18868 m= 168 mr = 2325 m= 0 mr = 45 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 31746 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 192 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 22640 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) : 0.5794648 object centre at (A) : 12.86200 48.33400 -45.18000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4390805E-03 1.3870216E-02 midg,1,midg; midg,igrid,midg 3.7628278E-04 -2.9617637E-02 1,midg,midg; igrid,midg,midg -1.6777866E-02 -3.7592445E-02 gauss-seidel spectral radius is 0.9984161 estimated iterations to convergence 199 setup time was (sec) 0.9400000 now iterating at: 06:56:52 rms-change max change #iterations 3.857408 162.2986 at 10iterations 1.698550 64.19762 at 20iterations 0.7523862 26.06121 at 30iterations 0.3330213 11.63687 at 40iterations 0.1475669 5.608694 at 50iterations 6.5262362E-02 2.079926 at 60iterations 2.8829681E-02 0.9475632 at 70iterations 1.2743907E-02 0.4011230 at 80iterations 5.6663668E-03 0.1794281 at 90iterations 2.5224208E-03 8.9632034E-02 at 100iterations 1.1341271E-03 3.6357880E-02 at 110iterations 5.2108342E-04 1.9378662E-02 at 120iterations finished qdiffx linear iterations at : 06:57:03 total time elapsed so far: 11.86000 # loops : 120 mean,max change (kT/e) : 5.2108342E-04 1.9378662E-02 energy calculations done at 11.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.03000 DelPhi exited at 06:57:03 12.036u 0.516s 0:12.91 97.1% 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 06:57:03 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3059 !!! WARNING: UMP 317 has a net charge of -0.1000 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: 2.607592 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): -17.85600 43.58000 ymin,ymax (A): 19.10800 77.56000 zmin,zma (A): -70.41200 -19.94800 x,y,z range (A): 61.43600 58.45200 50.46400 scale (grids/A): 2.607592 object centre (A): 12.86200 48.33400 -45.18000 number of atom coordinates read : 3059 total number of charged atoms : 2915 net assigned charge : -5.099980 assigned positive charge : 448.3334 centred at (gu) : 90.22581 89.53426 89.38728 assigned negative charge : -453.4339 centred at (gu) : 90.14780 90.62866 89.31730 start vw surface at 0.1300000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 166871 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26760 grid for indexing accessible points = 1.400000 m= 83501 mr = 119685 m= 30544 mr = 67402 m= 6701 mr = 24295 m= 672 mr = 4901 m= 26 mr = 427 m= 0 mr = 8 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.600000 number of dielectric boundary points 71597 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 23310 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) : 1.738394 object centre at (A) : 12.86200 48.33400 -45.18000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1025343 0.2602144 midg,1,midg; midg,igrid,midg -6.3769460E-02 -0.3021404 1,midg,midg; igrid,midg,midg -0.1936011 -0.5022154 gauss-seidel spectral radius is 0.9992102 estimated iterations to convergence 281 setup time was (sec) 1.980000 now iterating at: 06:57:06 rms-change max change #iterations 9.522216 354.7695 at 10iterations 5.455451 139.7337 at 20iterations 3.110012 69.62253 at 30iterations 1.767328 36.20499 at 40iterations 1.000130 23.25868 at 50iterations 0.5661087 11.23485 at 60iterations 0.3198179 6.486694 at 70iterations 0.1809627 3.240567 at 80iterations 0.1018568 1.939083 at 90iterations 5.7518799E-02 1.182853 at 100iterations 3.2375492E-02 0.6589050 at 110iterations 1.8246725E-02 0.3428822 at 120iterations 1.0279681E-02 0.2020603 at 130iterations 5.7987571E-03 0.1111231 at 140iterations 3.2747886E-03 6.2953949E-02 at 150iterations 1.8447285E-03 3.3098221E-02 at 160iterations 1.0425049E-03 2.0244598E-02 at 170iterations 5.8955845E-04 1.1934280E-02 at 180iterations finished qdiffx linear iterations at : 06:57:24 total time elapsed so far: 20.37000 # loops : 180 mean,max change (kT/e) : 5.8955845E-04 1.1934280E-02 energy calculations done at 20.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.53000 DelPhi exited at 06:57:25 20.534u 0.538s 0:21.65 97.2% 0+0k 0+0io 0pf+0w