Mon Oct 10 17:04:55 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 Mon Oct 10 2011 at 17:04:55 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2684 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 0.5723749 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): -11.31600 50.88100 ymin,ymax (A): -26.31400 17.08300 zmin,zma (A): -41.89100 5.132000 x,y,z range (A): 62.19700 43.39700 47.02300 scale (grids/A): 0.5723749 object centre (A): 19.78250 -4.615500 -18.37950 number of atom coordinates read : 2684 total number of charged atoms : 2543 net assigned charge : -0.4859765 assigned positive charge : 404.6105 centred at (gu) : 89.26743 89.89956 89.83331 assigned negative charge : -405.0975 centred at (gu) : 89.30733 89.78398 89.74193 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5794 nv = 96 ne = 84 npr = 53412 no. pairs analyzed = 53412 no. exposed pairs = 3729 no. arc points = 26297 no. surface atoms = 1251 nbur = 1433 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 247 mr = 2786 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3250 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2714 ## 338 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7448 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5769112E-09 1.2717891E-09 midg,1,midg; midg,igrid,midg -1.9468438E-09 1.6501449E-09 1,midg,midg; igrid,midg,midg 6.4228856E-10 -5.8968225E-10 gauss-seidel spectral radius is 0.9842315 estimated iterations to convergence 65 setup time was (sec) 0.5900000 now iterating at: 17:04:56 rms-change max change #iterations 8.5138120E-02 14.14406 at 10iterations 6.4591668E-03 1.223777 at 20iterations 4.7870041E-04 0.1036763 at 30iterations 3.6333589E-05 6.4859390E-03 at 40iterations 2.7455155E-06 4.2200089E-04 at 50iterations finished qdiffx linear iterations at : 17:04:59 total time elapsed so far: 4.270000 # loops : 50 mean,max change (kT/e) : 2.7455155E-06 4.2200089E-04 energy calculations done at 4.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.430000 DelPhi exited at 17:05:00 4.438u 0.395s 0:05.54 87.0% 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 Mon Oct 10 2011 at 17:05:00 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2684 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 1.717125 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): -11.31600 50.88100 ymin,ymax (A): -26.31400 17.08300 zmin,zma (A): -41.89100 5.132000 x,y,z range (A): 62.19700 43.39700 47.02300 scale (grids/A): 1.717125 object centre (A): 19.78250 -4.615500 -18.37950 number of atom coordinates read : 2684 total number of charged atoms : 2543 net assigned charge : -0.4859765 assigned positive charge : 404.6105 centred at (gu) : 87.80152 89.69806 89.49916 assigned negative charge : -405.0975 centred at (gu) : 87.92186 89.35189 89.22533 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 63328 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26297 grid for indexing accessible points = 1.400000 m= 18864 mr = 40895 m= 2094 mr = 12276 m= 58 mr = 912 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 30258 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 227 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 19670 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) : 0.5723749 object centre at (A) : 19.78250 -4.615500 -18.37950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2228052E-02 6.9107930E-03 midg,1,midg; midg,igrid,midg -6.6861748E-03 1.9733510E-03 1,midg,midg; igrid,midg,midg 8.8546965E-03 3.8316050E-03 gauss-seidel spectral radius is 0.9983404 estimated iterations to convergence 195 setup time was (sec) 0.7900000 now iterating at: 17:05:02 rms-change max change #iterations 3.508043 181.2665 at 10iterations 1.500672 62.95027 at 20iterations 0.6497531 23.04878 at 30iterations 0.2808343 10.67778 at 40iterations 0.1212311 3.985241 at 50iterations 5.2286353E-02 1.759118 at 60iterations 2.2687078E-02 0.8079314 at 70iterations 9.7724255E-03 0.3535175 at 80iterations 4.2394442E-03 0.1473026 at 90iterations 1.8337108E-03 7.0047379E-02 at 100iterations 7.8999915E-04 2.9251099E-02 at 110iterations 3.4302202E-04 1.2746811E-02 at 120iterations finished qdiffx linear iterations at : 17:05:11 total time elapsed so far: 10.15000 # loops : 120 mean,max change (kT/e) : 3.4302202E-04 1.2746811E-02 energy calculations done at 10.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.32000 DelPhi exited at 17:05:12 10.320u 0.443s 0:11.19 96.1% 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 Mon Oct 10 2011 at 17:05:12 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2684 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 2.575687 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): -11.31600 50.88100 ymin,ymax (A): -26.31400 17.08300 zmin,zma (A): -41.89100 5.132000 x,y,z range (A): 62.19700 43.39700 47.02300 scale (grids/A): 2.575687 object centre (A): 19.78250 -4.615500 -18.37950 number of atom coordinates read : 2684 total number of charged atoms : 2543 net assigned charge : -0.4859765 assigned positive charge : 404.6105 centred at (gu) : 86.70217 89.54694 89.24865 assigned negative charge : -405.0975 centred at (gu) : 86.88277 89.02776 88.83797 start vw surface at 0.1200000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 147006 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26297 grid for indexing accessible points = 1.400000 m= 64952 mr = 100824 m= 18694 mr = 49515 m= 3082 mr = 13388 m= 230 mr = 1887 m= 5 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.260000 number of dielectric boundary points 68260 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 20334 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) : 1.717125 object centre at (A) : 19.78250 -4.615500 -18.37950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1579363 0.1103562 midg,1,midg; midg,igrid,midg -6.7834377E-02 1.4922550E-02 1,midg,midg; igrid,midg,midg 0.1664481 0.2380184 gauss-seidel spectral radius is 0.9991874 estimated iterations to convergence 277 setup time was (sec) 1.560000 now iterating at: 17:05:14 rms-change max change #iterations 8.973526 332.8116 at 10iterations 5.142566 141.0148 at 20iterations 2.919843 74.17207 at 30iterations 1.651937 40.42221 at 40iterations 0.9315375 23.08116 at 50iterations 0.5238708 11.40795 at 60iterations 0.2943533 6.420263 at 70iterations 0.1646051 3.569193 at 80iterations 9.2109598E-02 1.879694 at 90iterations 5.1501229E-02 1.020479 at 100iterations 2.8823385E-02 0.6204700 at 110iterations 1.6107664E-02 0.3464508 at 120iterations 8.9989193E-03 0.1783266 at 130iterations 5.0266334E-03 0.1053348 at 140iterations 2.8066647E-03 5.7774782E-02 at 150iterations 1.5676856E-03 3.3278465E-02 at 160iterations 8.7321451E-04 1.8317223E-02 at 170iterations 4.8838690E-04 1.0540009E-02 at 180iterations finished qdiffx linear iterations at : 17:05:29 total time elapsed so far: 17.08000 # loops : 180 mean,max change (kT/e) : 4.8838690E-04 1.0540009E-02 energy calculations done at 17.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.25000 DelPhi exited at 17:05:30 17.256u 0.495s 0:18.51 95.8% 0+0k 0+0io 0pf+0w