Tue Oct 11 04:21:44 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+sph.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 = amb.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 04:21:44 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2565 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6639932 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): -14.90500 29.32700 ymin,ymax (A): 7.561000 51.81800 zmin,zma (A): 25.47600 79.09100 x,y,z range (A): 44.23200 44.25700 53.61501 scale (grids/A): 0.6639932 object centre (A): 7.211000 29.68950 52.28350 number of atom coordinates read : 2565 total number of charged atoms : 2416 net assigned charge : 4.162024 assigned positive charge : 383.4079 centred at (gu) : 90.66529 91.03133 89.04810 assigned negative charge : -379.2466 centred at (gu) : 91.00312 90.80280 89.12016 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7616 nv = 96 ne = 84 npr = 52788 no. pairs analyzed = 52788 no. exposed pairs = 3060 no. arc points = 21177 no. surface atoms = 1027 nbur = 1538 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 451 mr = 4431 m= 2 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 55 time to turn everything in is 0.2900000 number of dielectric boundary points 3572 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2051 ## 195 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8907 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2938690E-08 -2.9537777E-09 midg,1,midg; midg,igrid,midg -3.0666662E-08 7.3786502E-08 1,midg,midg; igrid,midg,midg 7.0870925E-08 -7.2714414E-08 gauss-seidel spectral radius is 0.9882365 estimated iterations to convergence 75 setup time was (sec) 0.5900000 now iterating at: 04:21:45 rms-change max change #iterations 0.1717125 23.48117 at 10iterations 1.8769246E-02 2.552711 at 20iterations 2.0830694E-03 0.3051033 at 30iterations 2.6812707E-04 3.9230347E-02 at 40iterations 5.1231655E-05 6.2179565E-03 at 50iterations finished qdiffx linear iterations at : 04:21:48 total time elapsed so far: 3.920000 # loops : 50 mean,max change (kT/e) : 5.1231655E-05 6.2179565E-03 energy calculations done at 3.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.100000 DelPhi exited at 04:21:49 4.106u 0.419s 0:04.97 90.7% 0+0k 0+0io 5pf+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 04:21:49 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2565 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.991980 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): -14.90500 29.32700 ymin,ymax (A): 7.561000 51.81800 zmin,zma (A): 25.47600 79.09100 x,y,z range (A): 44.23200 44.25700 53.61501 scale (grids/A): 1.991980 object centre (A): 7.211000 29.68950 52.28350 number of atom coordinates read : 2565 total number of charged atoms : 2416 net assigned charge : 4.162024 assigned positive charge : 383.4079 centred at (gu) : 91.99529 93.09338 87.14375 assigned negative charge : -379.2466 centred at (gu) : 93.00941 92.40829 87.36019 start vw surface at 0.1200000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 82146 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21177 grid for indexing accessible points = 1.400000 m= 31438 mr = 58792 m= 5382 mr = 23906 m= 382 mr = 3548 m= 5 mr = 158 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 2445 time to turn everything in is 0.6500000 number of dielectric boundary points 32949 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 19107 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) : 0.6639932 object centre at (A) : 7.211000 29.68950 52.28350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1226453E-02 -1.0280705E-02 midg,1,midg; midg,igrid,midg -1.0289351E-02 4.4290848E-02 1,midg,midg; igrid,midg,midg 6.2221810E-02 -5.6106646E-02 gauss-seidel spectral radius is 0.9987408 estimated iterations to convergence 223 setup time was (sec) 1.000000 now iterating at: 04:21:50 rms-change max change #iterations 4.600170 186.2716 at 10iterations 2.224838 73.42549 at 20iterations 1.073702 35.47148 at 30iterations 0.5179331 15.32257 at 40iterations 0.2514094 8.564796 at 50iterations 0.1214454 3.679462 at 60iterations 5.8710963E-02 1.797352 at 70iterations 2.8361464E-02 0.8975523 at 80iterations 1.3719946E-02 0.3826199 at 90iterations 6.6272970E-03 0.1851425 at 100iterations 3.2258183E-03 0.1025124 at 110iterations 1.5641657E-03 4.5011520E-02 at 120iterations finished qdiffx linear iterations at : 04:21:59 total time elapsed so far: 9.490000 # loops : 120 mean,max change (kT/e) : 1.5641657E-03 4.5011520E-02 energy calculations done at 9.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.670000 DelPhi exited at 04:21:59 9.680u 0.455s 0:10.64 95.2% 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 Tue Oct 11 2011 at 04:21:59 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2565 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.987969 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): -14.90500 29.32700 ymin,ymax (A): 7.561000 51.81800 zmin,zma (A): 25.47600 79.09100 x,y,z range (A): 44.23200 44.25700 53.61501 scale (grids/A): 2.987969 object centre (A): 7.211000 29.68950 52.28350 number of atom coordinates read : 2565 total number of charged atoms : 2416 net assigned charge : 4.162024 assigned positive charge : 383.4079 centred at (gu) : 92.99274 94.63998 85.71554 assigned negative charge : -379.2466 centred at (gu) : 94.51393 93.61223 86.04019 start vw surface at 0.1100000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 189920 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21177 grid for indexing accessible points = 1.400000 m= 100356 mr = 141895 m= 38195 mr = 83718 m= 9839 mr = 31330 m= 1611 mr = 7657 m= 106 mr = 1107 m= 5 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 8830 time to turn everything in is 1.710000 number of dielectric boundary points 74262 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.860000 number of grid points assigned charge 19317 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) : 1.991980 object centre at (A) : 7.211000 29.68950 52.28350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4299620 -1.2474650E-02 midg,1,midg; midg,igrid,midg -0.1046991 0.3541829 1,midg,midg; igrid,midg,midg 0.5173710 -0.6024926 gauss-seidel spectral radius is 0.9992796 estimated iterations to convergence 294 setup time was (sec) 2.050000 now iterating at: 04:22:02 rms-change max change #iterations 10.43947 442.5229 at 10iterations 6.123139 129.9579 at 20iterations 3.590315 64.76202 at 30iterations 2.098351 39.46503 at 40iterations 1.224026 25.23330 at 50iterations 0.7135400 12.26293 at 60iterations 0.4156854 7.241779 at 70iterations 0.2419134 4.629686 at 80iterations 0.1408911 2.831157 at 90iterations 8.1825785E-02 1.368668 at 100iterations 4.7540456E-02 0.8701706 at 110iterations 2.7655000E-02 0.4677229 at 120iterations 1.6118381E-02 0.2717339 at 130iterations 9.3997177E-03 0.1592369 at 140iterations 5.5091740E-03 0.1088867 at 150iterations 3.2578749E-03 6.2637329E-02 at 160iterations 1.9545602E-03 3.3596039E-02 at 170iterations 1.2015416E-03 2.5600433E-02 at 180iterations finished qdiffx linear iterations at : 04:22:16 total time elapsed so far: 16.49000 # loops : 180 mean,max change (kT/e) : 1.2015416E-03 2.5600433E-02 energy calculations done at 16.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.66000 DelPhi exited at 04:22:17 16.668u 0.487s 0:17.61 97.3% 0+0k 0+0io 0pf+0w