Sun Oct 9 10:28:50 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 10:28:50 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2216 !!! WARNING: HIR 524 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: 0.6223776 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): -1.503000 49.44300 ymin,ymax (A): -26.17600 31.02400 zmin,zma (A): -5.456000 47.90100 x,y,z range (A): 50.94600 57.20000 53.35700 scale (grids/A): 0.6223776 object centre (A): 23.97000 2.424001 21.22250 number of atom coordinates read : 2216 total number of charged atoms : 2079 net assigned charge : 2.514015 assigned positive charge : 323.5825 centred at (gu) : 90.23980 90.65678 91.08316 assigned negative charge : -321.0693 centred at (gu) : 90.26270 90.50352 91.08291 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5866 nv = 96 ne = 84 npr = 43994 no. pairs analyzed = 43994 no. exposed pairs = 2989 no. arc points = 21477 no. surface atoms = 996 nbur = 1220 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 330 mr = 2965 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2700000 number of dielectric boundary points 3196 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2129 ## 203 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7027 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6740324E-09 2.6854328E-09 midg,1,midg; midg,igrid,midg -6.0804264E-09 1.2707400E-08 1,midg,midg; igrid,midg,midg 3.2863907E-09 8.0153240E-10 gauss-seidel spectral radius is 0.9866078 estimated iterations to convergence 71 setup time was (sec) 0.5100000 now iterating at: 10:28:51 rms-change max change #iterations 0.1184031 21.36999 at 10iterations 1.0688750E-02 1.628222 at 20iterations 9.7763375E-04 0.1556168 at 30iterations 9.1266062E-05 1.4686584E-02 at 40iterations 8.5285546E-06 1.4424324E-03 at 50iterations finished qdiffx linear iterations at : 10:28:53 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 8.5285546E-06 1.4424324E-03 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 10:28:54 3.275u 0.189s 0:03.82 90.3% 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 Sun Oct 9 2011 at 10:28:54 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2216 !!! WARNING: HIR 524 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.867133 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): -1.503000 49.44300 ymin,ymax (A): -26.17600 31.02400 zmin,zma (A): -5.456000 47.90100 x,y,z range (A): 50.94600 57.20000 53.35700 scale (grids/A): 1.867133 object centre (A): 23.97000 2.424001 21.22250 number of atom coordinates read : 2216 total number of charged atoms : 2079 net assigned charge : 2.514015 assigned positive charge : 323.5825 centred at (gu) : 90.71909 91.97002 93.24925 assigned negative charge : -321.0693 centred at (gu) : 90.78828 91.51075 93.24892 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 63268 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21477 grid for indexing accessible points = 1.400000 m= 21266 mr = 41495 m= 3388 mr = 15023 m= 225 mr = 2120 m= 3 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 467 time to turn everything in is 0.4800000 number of dielectric boundary points 29457 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 137 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 16319 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) : 0.6223776 object centre at (A) : 23.97000 2.424001 21.22250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3804131E-02 3.4530427E-02 midg,1,midg; midg,igrid,midg -5.4630009E-03 2.8073948E-02 1,midg,midg; igrid,midg,midg -1.0220901E-02 -1.0736360E-02 gauss-seidel spectral radius is 0.9985549 estimated iterations to convergence 209 setup time was (sec) 0.7600000 now iterating at: 10:28:55 rms-change max change #iterations 3.678448 162.5808 at 10iterations 1.683940 72.05271 at 20iterations 0.7710034 26.80060 at 30iterations 0.3515542 13.87455 at 40iterations 0.1608182 7.226746 at 50iterations 7.3867291E-02 2.471348 at 60iterations 3.3734821E-02 1.196661 at 70iterations 1.5468273E-02 0.5641880 at 80iterations 7.0795892E-03 0.2518024 at 90iterations 3.2449600E-03 0.1272583 at 100iterations 1.4890719E-03 5.6756884E-02 at 110iterations 6.7762949E-04 2.2620201E-02 at 120iterations finished qdiffx linear iterations at : 10:29:01 total time elapsed so far: 7.190000 # loops : 120 mean,max change (kT/e) : 6.7762949E-04 2.2620201E-02 energy calculations done at 7.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.350000 DelPhi exited at 10:29:02 7.351u 0.210s 0:07.93 95.3% 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 Sun Oct 9 2011 at 10:29:02 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2216 !!! WARNING: HIR 524 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.800699 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): -1.503000 49.44300 ymin,ymax (A): -26.17600 31.02400 zmin,zma (A): -5.456000 47.90100 x,y,z range (A): 50.94600 57.20000 53.35700 scale (grids/A): 2.800699 object centre (A): 23.97000 2.424001 21.22250 number of atom coordinates read : 2216 total number of charged atoms : 2079 net assigned charge : 2.514015 assigned positive charge : 323.5825 centred at (gu) : 91.07858 92.95507 94.87382 assigned negative charge : -321.0693 centred at (gu) : 91.18251 92.26616 94.87357 start vw surface at 0.1400000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 146291 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21477 grid for indexing accessible points = 1.400000 m= 68932 mr = 101416 m= 24698 mr = 54608 m= 6208 mr = 19462 m= 936 mr = 4668 m= 57 mr = 601 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 1534 time to turn everything in is 1.120000 number of dielectric boundary points 66352 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 16627 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) : 1.867133 object centre at (A) : 23.97000 2.424001 21.22250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2227016 0.4493965 midg,1,midg; midg,igrid,midg -8.1418104E-02 0.2446704 1,midg,midg; igrid,midg,midg -0.1812081 -0.1487938 gauss-seidel spectral radius is 0.9992351 estimated iterations to convergence 285 setup time was (sec) 1.420000 now iterating at: 10:29:04 rms-change max change #iterations 8.681108 341.1389 at 10iterations 4.996584 132.5745 at 20iterations 2.865575 64.56331 at 30iterations 1.640936 33.89380 at 40iterations 0.9337400 18.44443 at 50iterations 0.5336305 11.05709 at 60iterations 0.3034918 6.066078 at 70iterations 0.1729691 3.995771 at 80iterations 9.8560847E-02 2.093800 at 90iterations 5.5968910E-02 1.117556 at 100iterations 3.1868316E-02 0.6441841 at 110iterations 1.8107904E-02 0.3605390 at 120iterations 1.0302414E-02 0.2066956 at 130iterations 5.8593894E-03 0.1122942 at 140iterations 3.3380603E-03 6.2674284E-02 at 150iterations 1.8977303E-03 3.5333633E-02 at 160iterations 1.0805990E-03 2.2756472E-02 at 170iterations 6.1493408E-04 1.2607574E-02 at 180iterations finished qdiffx linear iterations at : 10:29:14 total time elapsed so far: 11.53000 # loops : 180 mean,max change (kT/e) : 6.1493408E-04 1.2607574E-02 energy calculations done at 11.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.70000 DelPhi exited at 10:29:14 11.705u 0.231s 0:12.29 97.0% 0+0k 0+0io 0pf+0w