Sun Oct 9 12:00:21 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 12:00:21 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2414 !!! 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6775919 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): -6.626000 44.59300 ymin,ymax (A): -14.34300 38.19600 zmin,zma (A): 2.453000 44.90500 x,y,z range (A): 51.21900 52.53900 42.45200 scale (grids/A): 0.6775919 object centre (A): 18.98350 11.92650 23.67900 number of atom coordinates read : 2414 total number of charged atoms : 2268 net assigned charge : 4.406024 assigned positive charge : 369.9880 centred at (gu) : 89.74637 90.87452 90.49369 assigned negative charge : -365.5825 centred at (gu) : 89.71890 91.03384 90.58719 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7476 nv = 96 ne = 84 npr = 48317 no. pairs analyzed = 48317 no. exposed pairs = 3036 no. arc points = 21617 no. surface atoms = 1013 nbur = 1401 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 443 mr = 4100 m= 2 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.1900000 number of dielectric boundary points 3749 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2144 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8699 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.0925038E-08 -9.8575610E-09 midg,1,midg; midg,igrid,midg 5.3373682E-08 -3.4205822E-08 1,midg,midg; igrid,midg,midg 1.1035513E-08 2.5087591E-08 gauss-seidel spectral radius is 0.9886902 estimated iterations to convergence 77 setup time was (sec) 0.3800000 now iterating at: 12:00:21 rms-change max change #iterations 0.1779219 23.94193 at 10iterations 2.0569067E-02 2.763185 at 20iterations 2.9509750E-03 0.4469795 at 30iterations 6.7606458E-04 0.1090736 at 40iterations 2.1718672E-04 3.4919739E-02 at 50iterations finished qdiffx linear iterations at : 12:00:24 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 2.1718672E-04 3.4919739E-02 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 12:00:25 3.388u 0.186s 0:03.85 92.4% 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 12:00:25 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2414 !!! 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.032776 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): -6.626000 44.59300 ymin,ymax (A): -14.34300 38.19600 zmin,zma (A): 2.453000 44.90500 x,y,z range (A): 51.21900 52.53900 42.45200 scale (grids/A): 2.032776 object centre (A): 18.98350 11.92650 23.67900 number of atom coordinates read : 2414 total number of charged atoms : 2268 net assigned charge : 4.406024 assigned positive charge : 369.9880 centred at (gu) : 89.23842 92.62338 91.48055 assigned negative charge : -365.5825 centred at (gu) : 89.15659 93.10126 91.76128 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79453 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21617 grid for indexing accessible points = 1.400000 m= 30367 mr = 55042 m= 5233 mr = 22487 m= 431 mr = 3292 m= 8 mr = 212 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1145 time to turn everything in is 0.4000000 number of dielectric boundary points 34459 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 128 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 17991 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) : 0.6775919 object centre at (A) : 18.98350 11.92650 23.67900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0906945E-02 7.8113736E-03 midg,1,midg; midg,igrid,midg 9.4761774E-03 -6.4833149E-02 1,midg,midg; igrid,midg,midg 3.6550552E-02 4.0647290E-03 gauss-seidel spectral radius is 0.9987808 estimated iterations to convergence 227 setup time was (sec) 0.6100000 now iterating at: 12:00:26 rms-change max change #iterations 4.651603 208.9589 at 10iterations 2.250610 88.21939 at 20iterations 1.099220 35.35356 at 30iterations 0.5384310 17.87079 at 40iterations 0.2626398 8.009168 at 50iterations 0.1279711 3.718772 at 60iterations 6.3032717E-02 2.078916 at 70iterations 3.0829376E-02 0.8863099 at 80iterations 1.5337027E-02 0.5142822 at 90iterations 7.7223722E-03 0.2588024 at 100iterations 3.9628092E-03 0.1274109 at 110iterations 2.1270313E-03 7.7751160E-02 at 120iterations finished qdiffx linear iterations at : 12:00:33 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 2.1270313E-03 7.7751160E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 12:00:33 7.859u 0.209s 0:08.33 96.6% 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 Sun Oct 9 2011 at 12:00:33 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2414 !!! 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.049163 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): -6.626000 44.59300 ymin,ymax (A): -14.34300 38.19600 zmin,zma (A): 2.453000 44.90500 x,y,z range (A): 51.21900 52.53900 42.45200 scale (grids/A): 3.049163 object centre (A): 18.98350 11.92650 23.67900 number of atom coordinates read : 2414 total number of charged atoms : 2268 net assigned charge : 4.406024 assigned positive charge : 369.9880 centred at (gu) : 88.85753 93.93479 92.22066 assigned negative charge : -365.5825 centred at (gu) : 88.73480 94.65185 92.64191 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 183079 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21617 grid for indexing accessible points = 1.400000 m= 96068 mr = 132675 m= 36826 mr = 79000 m= 9621 mr = 29494 m= 1749 mr = 7256 m= 183 mr = 1262 m= 2 mr = 120 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 4216 time to turn everything in is 1.050000 number of dielectric boundary points 77721 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 18144 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) : 2.032776 object centre at (A) : 18.98350 11.92650 23.67900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4433025 -3.0340914E-02 midg,1,midg; midg,igrid,midg 0.2377280 -0.7681529 1,midg,midg; igrid,midg,midg 0.3913701 -0.1667365 gauss-seidel spectral radius is 0.9992871 estimated iterations to convergence 296 setup time was (sec) 1.290000 now iterating at: 12:00:35 rms-change max change #iterations 10.64600 494.9831 at 10iterations 6.278675 121.5016 at 20iterations 3.700018 77.36499 at 30iterations 2.176481 41.87999 at 40iterations 1.273765 24.43058 at 50iterations 0.7444000 15.13636 at 60iterations 0.4358102 8.095860 at 70iterations 0.2552199 4.445964 at 80iterations 0.1490778 2.449129 at 90iterations 8.7061964E-02 1.490301 at 100iterations 5.0965939E-02 0.8876209 at 110iterations 2.9976746E-02 0.6098747 at 120iterations 1.7829310E-02 0.3277378 at 130iterations 1.0826807E-02 0.2431870 at 140iterations 6.7886077E-03 0.1307945 at 150iterations 4.4788625E-03 9.2304230E-02 at 160iterations 3.1451855E-03 6.6089630E-02 at 170iterations 2.3393170E-03 5.0708771E-02 at 180iterations finished qdiffx linear iterations at : 12:00:46 total time elapsed so far: 12.70000 # loops : 180 mean,max change (kT/e) : 2.3393170E-03 5.0708771E-02 energy calculations done at 12.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.83000 DelPhi exited at 12:00:46 12.830u 0.206s 0:13.31 97.8% 0+0k 0+0io 0pf+0w