Tue Oct 11 03:45:31 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 03:45:31 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: 362 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2794 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6408294 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): -10.61200 36.61900 ymin,ymax (A): -26.45600 23.38700 zmin,zma (A): -10.32600 45.22700 x,y,z range (A): 47.23100 49.84300 55.55300 scale (grids/A): 0.6408294 object centre (A): 13.00350 -1.534500 17.45050 number of atom coordinates read : 2794 total number of charged atoms : 2631 net assigned charge : 1.588024 assigned positive charge : 426.5437 centred at (gu) : 90.03809 89.86280 91.81983 assigned negative charge : -424.9562 centred at (gu) : 89.81551 89.73827 91.79008 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7421 nv = 96 ne = 84 npr = 57917 no. pairs analyzed = 57917 no. exposed pairs = 3290 no. arc points = 22617 no. surface atoms = 1110 nbur = 1684 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 381 mr = 4212 m= 2 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.2100000 number of dielectric boundary points 3531 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2236 ## 214 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9106 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0107145E-09 9.1885424E-09 midg,1,midg; midg,igrid,midg -1.4529190E-08 1.7801092E-08 1,midg,midg; igrid,midg,midg -2.7129749E-08 3.0885424E-08 gauss-seidel spectral radius is 0.9873924 estimated iterations to convergence 73 setup time was (sec) 0.4100000 now iterating at: 03:45:32 rms-change max change #iterations 0.1549152 19.96194 at 10iterations 1.5618279E-02 2.341763 at 20iterations 1.5560328E-03 0.2070580 at 30iterations 1.6623984E-04 2.1625519E-02 at 40iterations 2.1287849E-05 3.3035278E-03 at 50iterations finished qdiffx linear iterations at : 03:45:35 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 2.1287849E-05 3.3035278E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 03:45:35 3.428u 0.162s 0:04.09 87.5% 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 Tue Oct 11 2011 at 03:45:35 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: 362 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2794 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.922488 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): -10.61200 36.61900 ymin,ymax (A): -26.45600 23.38700 zmin,zma (A): -10.32600 45.22700 x,y,z range (A): 47.23100 49.84300 55.55300 scale (grids/A): 1.922488 object centre (A): 13.00350 -1.534500 17.45050 number of atom coordinates read : 2794 total number of charged atoms : 2631 net assigned charge : 1.588024 assigned positive charge : 426.5437 centred at (gu) : 90.11382 89.58778 95.45904 assigned negative charge : -424.9562 centred at (gu) : 89.44598 89.21430 95.36978 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 80471 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22617 grid for indexing accessible points = 1.400000 m= 28929 mr = 56942 m= 4354 mr = 21574 m= 229 mr = 2706 m= 3 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 993 time to turn everything in is 0.3900000 number of dielectric boundary points 32689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 136 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 20712 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) : 0.6408294 object centre at (A) : 13.00350 -1.534500 17.45050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6118230E-02 6.4053009E-03 midg,1,midg; midg,igrid,midg -2.1764237E-02 -4.9616424E-03 1,midg,midg; igrid,midg,midg -1.1787750E-02 5.3938795E-02 gauss-seidel spectral radius is 0.9986723 estimated iterations to convergence 217 setup time was (sec) 0.6100000 now iterating at: 03:45:36 rms-change max change #iterations 4.610959 183.0245 at 10iterations 2.176055 68.97112 at 20iterations 1.034075 33.44103 at 30iterations 0.4918559 15.75239 at 40iterations 0.2329382 6.985873 at 50iterations 0.1105504 3.862698 at 60iterations 5.2441776E-02 1.553741 at 70iterations 2.4877086E-02 0.7731171 at 80iterations 1.1802330E-02 0.3695450 at 90iterations 5.5950792E-03 0.1675491 at 100iterations 2.6486344E-03 7.6171875E-02 at 110iterations 1.2557247E-03 3.6998749E-02 at 120iterations finished qdiffx linear iterations at : 03:45:43 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 1.2557247E-03 3.6998749E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 03:45:44 7.864u 0.211s 0:08.38 96.3% 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 03:45:44 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: 362 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2794 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.883733 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): -10.61200 36.61900 ymin,ymax (A): -26.45600 23.38700 zmin,zma (A): -10.32600 45.22700 x,y,z range (A): 47.23100 49.84300 55.55300 scale (grids/A): 2.883733 object centre (A): 13.00350 -1.534500 17.45050 number of atom coordinates read : 2794 total number of charged atoms : 2631 net assigned charge : 1.588024 assigned positive charge : 426.5437 centred at (gu) : 90.17048 89.38154 98.18841 assigned negative charge : -424.9562 centred at (gu) : 89.16890 88.82137 98.05475 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 186298 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22617 grid for indexing accessible points = 1.400000 m= 94453 mr = 137947 m= 33124 mr = 77880 m= 7662 mr = 26736 m= 1013 mr = 5687 m= 60 mr = 668 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 3149 time to turn everything in is 1.000000 number of dielectric boundary points 73670 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 21032 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) : 1.922488 object centre at (A) : 13.00350 -1.534500 17.45050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4345225 0.2245943 midg,1,midg; midg,igrid,midg -0.2323735 -0.1393397 1,midg,midg; igrid,midg,midg -5.8079127E-02 0.5047973 gauss-seidel spectral radius is 0.9992664 estimated iterations to convergence 291 setup time was (sec) 1.250000 now iterating at: 03:45:45 rms-change max change #iterations 10.66842 335.7130 at 10iterations 6.222808 170.1789 at 20iterations 3.619218 81.61082 at 30iterations 2.102115 39.72861 at 40iterations 1.216254 23.59070 at 50iterations 0.7050149 14.10271 at 60iterations 0.4066485 7.303272 at 70iterations 0.2353053 4.485600 at 80iterations 0.1360919 2.554613 at 90iterations 7.8494273E-02 1.530283 at 100iterations 4.5258366E-02 0.9255896 at 110iterations 2.6091855E-02 0.4690218 at 120iterations 1.5053386E-02 0.2692127 at 130iterations 8.6916015E-03 0.1551533 at 140iterations 5.0017638E-03 9.1743469E-02 at 150iterations 2.8922884E-03 5.0742209E-02 at 160iterations 1.6640202E-03 2.9586792E-02 at 170iterations 9.6032419E-04 1.7986298E-02 at 180iterations finished qdiffx linear iterations at : 03:45:57 total time elapsed so far: 12.75000 # loops : 180 mean,max change (kT/e) : 9.6032419E-04 1.7986298E-02 energy calculations done at 12.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.88000 DelPhi exited at 03:45:57 12.883u 0.219s 0:13.37 97.9% 0+0k 0+0io 0pf+0w