Wed Dec 21 14:21:33 PST 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 Wed Dec 21 2011 at 14:21:34 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 0.6497654 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): -5.057000 35.66000 ymin,ymax (A): -3.927000 48.60200 zmin,zma (A): -24.26700 30.52200 x,y,z range (A): 40.71700 52.52900 54.78900 scale (grids/A): 0.6497654 object centre (A): 15.30150 22.33750 3.127501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 290.6260 centred at (gu) : 90.34800 92.73941 90.29160 assigned negative charge : -288.6263 centred at (gu) : 90.48032 92.87753 90.20257 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5726 nv = 96 ne = 84 npr = 40444 no. pairs analyzed = 40444 no. exposed pairs = 2377 no. arc points = 17273 no. surface atoms = 808 nbur = 1156 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 313 mr = 3233 m= 0 mr = 43 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 44 time to turn everything in is 0.1700000 number of dielectric boundary points 2763 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1679 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 6613 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.3436486E-09 1.5086492E-08 midg,1,midg; midg,igrid,midg 1.1006161E-08 -2.0873008E-08 1,midg,midg; igrid,midg,midg 1.7554365E-08 -1.1501503E-08 gauss-seidel spectral radius is 0.9876711 estimated iterations to convergence 74 setup time was (sec) 0.4300000 now iterating at: 14:21:35 rms-change max change #iterations 0.1345510 21.07441 at 10iterations 1.3808518E-02 2.465672 at 20iterations 1.4196113E-03 0.2435913 at 30iterations 1.4394781E-04 2.1036148E-02 at 40iterations 1.4992089E-05 2.3460388E-03 at 50iterations finished qdiffx linear iterations at : 14:21:39 total time elapsed so far: 4.490000 # loops : 50 mean,max change (kT/e) : 1.4992089E-05 2.3460388E-03 energy calculations done at 4.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.620000 DelPhi exited at 14:21:47 4.623u 0.264s 0:14.98 32.5% 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 Wed Dec 21 2011 at 14:21:50 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 1.949296 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): -5.057000 35.66000 ymin,ymax (A): -3.927000 48.60200 zmin,zma (A): -24.26700 30.52200 x,y,z range (A): 40.71700 52.52900 54.78900 scale (grids/A): 1.949296 object centre (A): 15.30150 22.33750 3.127501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 290.6260 centred at (gu) : 91.04422 98.21828 90.87469 assigned negative charge : -288.6263 centred at (gu) : 91.44127 98.63274 90.60783 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 60789 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17273 grid for indexing accessible points = 1.400000 m= 23502 mr = 42071 m= 3854 mr = 18244 m= 224 mr = 2565 m= 4 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1479 time to turn everything in is 0.3200000 number of dielectric boundary points 25389 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 14470 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) : 0.6497654 object centre at (A) : 15.30150 22.33750 3.127501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2503644E-02 1.2506466E-02 midg,1,midg; midg,igrid,midg 3.3082847E-02 -1.6043222E-02 1,midg,midg; igrid,midg,midg 7.8027891E-03 -6.3650589E-03 gauss-seidel spectral radius is 0.9986185 estimated iterations to convergence 213 setup time was (sec) 0.5700000 now iterating at: 14:21:51 rms-change max change #iterations 3.776045 157.2418 at 10iterations 1.758596 73.21635 at 20iterations 0.8208439 29.26974 at 30iterations 0.3836996 13.94366 at 40iterations 0.1783961 5.757896 at 50iterations 8.3292194E-02 3.061895 at 60iterations 3.8790282E-02 1.289892 at 70iterations 1.8049510E-02 0.6062565 at 80iterations 8.4056556E-03 0.2708158 at 90iterations 3.9098291E-03 0.1496887 at 100iterations 1.8187958E-03 7.5307846E-02 at 110iterations 8.5249735E-04 3.1625271E-02 at 120iterations finished qdiffx linear iterations at : 14:22:01 total time elapsed so far: 10.66000 # loops : 120 mean,max change (kT/e) : 8.5249735E-04 3.1625271E-02 energy calculations done at 10.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.79000 DelPhi exited at 14:22:07 10.796u 0.262s 0:17.48 63.2% 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 Wed Dec 21 2011 at 14:22:09 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 2.923944 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): -5.057000 35.66000 ymin,ymax (A): -3.927000 48.60200 zmin,zma (A): -24.26700 30.52200 x,y,z range (A): 40.71700 52.52900 54.78900 scale (grids/A): 2.923944 object centre (A): 15.30150 22.33750 3.127501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 290.6260 centred at (gu) : 91.56640 102.3274 91.31212 assigned negative charge : -288.6263 centred at (gu) : 92.16180 102.9490 90.91168 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 140089 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17273 grid for indexing accessible points = 1.400000 m= 73966 mr = 101354 m= 29340 mr = 62032 m= 7040 mr = 24709 m= 993 mr = 5465 m= 68 mr = 692 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 4790 time to turn everything in is 0.7900000 number of dielectric boundary points 57215 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 14656 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) : 1.949296 object centre at (A) : 15.30150 22.33750 3.127501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.059910 3.3736493E-02 midg,1,midg; midg,igrid,midg 0.3090315 -0.1973508 1,midg,midg; igrid,midg,midg 4.7395762E-02 -3.7471984E-02 gauss-seidel spectral radius is 0.9992402 estimated iterations to convergence 286 setup time was (sec) 1.030000 now iterating at: 14:22:12 rms-change max change #iterations 8.822697 478.6737 at 10iterations 5.056334 139.6823 at 20iterations 2.891652 68.64641 at 30iterations 1.644989 33.90077 at 40iterations 0.9419234 19.37141 at 50iterations 0.5359993 11.14903 at 60iterations 0.3057105 6.044140 at 70iterations 0.1737267 3.355442 at 80iterations 9.8814838E-02 1.862617 at 90iterations 5.6182902E-02 1.163273 at 100iterations 3.2007355E-02 0.6574762 at 110iterations 1.8238468E-02 0.3931018 at 120iterations 1.0376017E-02 0.2095184 at 130iterations 5.9001422E-03 0.1169777 at 140iterations 3.3728674E-03 6.1977386E-02 at 150iterations 1.9164700E-03 3.6665916E-02 at 160iterations 1.0884862E-03 2.0849705E-02 at 170iterations 6.1851973E-04 1.1810541E-02 at 180iterations finished qdiffx linear iterations at : 14:22:23 total time elapsed so far: 12.25000 # loops : 180 mean,max change (kT/e) : 6.1851973E-04 1.1810541E-02 energy calculations done at 12.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.39000 DelPhi exited at 14:22:33 12.388u 0.222s 0:24.16 52.1% 0+0k 0+0io 0pf+0w