Sat Oct 15 12:58:11 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 15 2011 at 12:58:11 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2367 !!! WARNING: GLM 182 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6784312 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): -7.506000 44.68800 ymin,ymax (A): -14.05400 38.42000 zmin,zma (A): 2.077000 45.13500 x,y,z range (A): 52.19400 52.47400 43.05800 scale (grids/A): 0.6784312 object centre (A): 18.59100 12.18300 23.60600 number of atom coordinates read : 2367 total number of charged atoms : 2221 net assigned charge : 3.406020 assigned positive charge : 362.0292 centred at (gu) : 89.87082 90.77823 90.76543 assigned negative charge : -358.6236 centred at (gu) : 89.89474 90.91939 90.80779 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7412 nv = 96 ne = 84 npr = 47285 no. pairs analyzed = 47285 no. exposed pairs = 2944 no. arc points = 20840 no. surface atoms = 994 nbur = 1373 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 450 mr = 4134 m= 4 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3656 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1989 ## 180 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8431 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2940442E-08 2.4786455E-09 midg,1,midg; midg,igrid,midg 4.6758064E-08 -3.1764760E-08 1,midg,midg; igrid,midg,midg 2.2004869E-08 7.4285746E-09 gauss-seidel spectral radius is 0.9887154 estimated iterations to convergence 77 setup time was (sec) 0.4200000 now iterating at: 12:58:11 rms-change max change #iterations 0.1842398 27.60789 at 10iterations 2.1341365E-02 3.017746 at 20iterations 2.9507396E-03 0.4582291 at 30iterations 6.4016914E-04 0.1015549 at 40iterations 1.9137157E-04 3.0540466E-02 at 50iterations finished qdiffx linear iterations at : 12:58:15 total time elapsed so far: 3.730000 # loops : 50 mean,max change (kT/e) : 1.9137157E-04 3.0540466E-02 energy calculations done at 3.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.870000 DelPhi exited at 12:58:15 3.872u 0.232s 0:04.57 89.7% 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 15 2011 at 12:58:15 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2367 !!! WARNING: GLM 182 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.035294 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): -7.506000 44.68800 ymin,ymax (A): -14.05400 38.42000 zmin,zma (A): 2.077000 45.13500 x,y,z range (A): 52.19400 52.47400 43.05800 scale (grids/A): 2.035294 object centre (A): 18.59100 12.18300 23.60600 number of atom coordinates read : 2367 total number of charged atoms : 2221 net assigned charge : 3.406020 assigned positive charge : 362.0292 centred at (gu) : 89.61198 92.33396 92.29567 assigned negative charge : -358.6236 centred at (gu) : 89.68410 92.75782 92.42321 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 78748 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20840 grid for indexing accessible points = 1.400000 m= 30791 mr = 54754 m= 5606 mr = 23196 m= 451 mr = 3649 m= 7 mr = 237 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 244 time to turn everything in is 0.4200000 number of dielectric boundary points 33767 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 120 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 17574 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) : 0.6784312 object centre at (A) : 18.59100 12.18300 23.60600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9219718E-02 1.2292983E-02 midg,1,midg; midg,igrid,midg 1.1289448E-02 -3.9044980E-02 1,midg,midg; igrid,midg,midg 4.2193949E-02 -5.6618908E-03 gauss-seidel spectral radius is 0.9987790 estimated iterations to convergence 227 setup time was (sec) 0.7000000 now iterating at: 12:58:16 rms-change max change #iterations 4.639988 195.0838 at 10iterations 2.259217 83.19609 at 20iterations 1.100590 35.53554 at 30iterations 0.5394946 17.52893 at 40iterations 0.2622397 8.637939 at 50iterations 0.1282981 4.033906 at 60iterations 6.2745303E-02 1.846794 at 70iterations 3.0802792E-02 0.8771973 at 80iterations 1.5275087E-02 0.4478912 at 90iterations 7.6486222E-03 0.2581863 at 100iterations 3.9156470E-03 0.1174383 at 110iterations 2.0853381E-03 6.7647934E-02 at 120iterations finished qdiffx linear iterations at : 12:58:25 total time elapsed so far: 9.150000 # loops : 120 mean,max change (kT/e) : 2.0853381E-03 6.7647934E-02 energy calculations done at 9.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.280000 DelPhi exited at 12:58:25 9.286u 0.309s 0:09.88 96.9% 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 15 2011 at 12:58:25 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2367 !!! WARNING: GLM 182 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.052941 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): -7.506000 44.68800 ymin,ymax (A): -14.05400 38.42000 zmin,zma (A): 2.077000 45.13500 x,y,z range (A): 52.19400 52.47400 43.05800 scale (grids/A): 3.052941 object centre (A): 18.59100 12.18300 23.60600 number of atom coordinates read : 2367 total number of charged atoms : 2221 net assigned charge : 3.406020 assigned positive charge : 362.0292 centred at (gu) : 89.41788 93.50083 93.44345 assigned negative charge : -358.6236 centred at (gu) : 89.52604 94.13667 93.63474 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 181499 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20840 grid for indexing accessible points = 1.400000 m= 96538 mr = 131850 m= 37978 mr = 79815 m= 10277 mr = 31105 m= 1953 mr = 7972 m= 186 mr = 1424 m= 2 mr = 110 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 789 time to turn everything in is 1.190000 number of dielectric boundary points 76157 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 17762 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) : 2.035294 object centre at (A) : 18.59100 12.18300 23.60600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3905673 1.4391789E-02 midg,1,midg; midg,igrid,midg 0.2317620 -0.4289394 1,midg,midg; igrid,midg,midg 0.4186430 -0.1716363 gauss-seidel spectral radius is 0.9992856 estimated iterations to convergence 295 setup time was (sec) 1.540000 now iterating at: 12:58:27 rms-change max change #iterations 10.65161 397.6946 at 10iterations 6.301548 145.2302 at 20iterations 3.714530 73.63699 at 30iterations 2.188570 45.96117 at 40iterations 1.286161 24.97522 at 50iterations 0.7533053 13.33104 at 60iterations 0.4404279 7.681713 at 70iterations 0.2579051 4.673339 at 80iterations 0.1504202 2.622297 at 90iterations 8.8122055E-02 1.494360 at 100iterations 5.1731050E-02 0.9420624 at 110iterations 3.0471362E-02 0.5506015 at 120iterations 1.8129235E-02 0.3473740 at 130iterations 1.0995694E-02 0.2268162 at 140iterations 6.9287354E-03 0.1451721 at 150iterations 4.5833942E-03 0.1092033 at 160iterations 3.2237866E-03 6.8492889E-02 at 170iterations 2.4100854E-03 5.1044464E-02 at 180iterations finished qdiffx linear iterations at : 12:58:43 total time elapsed so far: 17.31000 # loops : 180 mean,max change (kT/e) : 2.4100854E-03 5.1044464E-02 energy calculations done at 17.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.43000 DelPhi exited at 12:58:43 17.435u 0.368s 0:18.16 97.9% 0+0k 0+0io 0pf+0w