Tue Oct 11 08:20:41 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+sph.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 = amb.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 08:20:41 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 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: 0.5174795 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): 15.68100 84.47600 ymin,ymax (A): 37.45400 93.32200 zmin,zma (A): -25.63000 23.49700 x,y,z range (A): 68.79500 55.86800 49.12700 scale (grids/A): 0.5174795 object centre (A): 50.07850 65.38800 -1.066500 number of atom coordinates read : 2581 total number of charged atoms : 2442 net assigned charge : -0.9999892 assigned positive charge : 383.5807 centred at (gu) : 84.88100 90.41002 89.96899 assigned negative charge : -384.5815 centred at (gu) : 84.97109 90.37984 90.01962 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4595 nv = 96 ne = 84 npr = 49807 no. pairs analyzed = 49807 no. exposed pairs = 3893 no. arc points = 28618 no. surface atoms = 1278 nbur = 1303 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 = 1.652000 m= 182 mr = 1931 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2845 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2766 ## 419 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 6106 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.3026057E-11 -1.1881399E-10 midg,1,midg; midg,igrid,midg -7.4203380E-11 2.9178642E-11 1,midg,midg; igrid,midg,midg 5.3842025E-10 -5.2020076E-11 gauss-seidel spectral radius is 0.9807573 estimated iterations to convergence 60 setup time was (sec) 0.5800000 now iterating at: 08:20:42 rms-change max change #iterations 5.0755955E-02 11.03616 at 10iterations 3.0186491E-03 0.6060581 at 20iterations 4.0613231E-04 9.7508430E-02 at 30iterations 1.1289836E-04 2.8860092E-02 at 40iterations 3.3996799E-05 8.7070465E-03 at 50iterations finished qdiffx linear iterations at : 08:20:46 total time elapsed so far: 4.470000 # loops : 50 mean,max change (kT/e) : 3.3996799E-05 8.7070465E-03 energy calculations done at 4.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.640000 DelPhi exited at 08:20:46 4.641u 0.392s 0:05.46 92.1% 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 Tue Oct 11 2011 at 08:20:46 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 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: 1.552438 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): 15.68100 84.47600 ymin,ymax (A): 37.45400 93.32200 zmin,zma (A): -25.63000 23.49700 x,y,z range (A): 68.79500 55.86800 49.12700 scale (grids/A): 1.552438 object centre (A): 50.07850 65.38800 -1.066500 number of atom coordinates read : 2581 total number of charged atoms : 2442 net assigned charge : -0.9999892 assigned positive charge : 383.5807 centred at (gu) : 74.64248 91.22960 89.90654 assigned negative charge : -384.5815 centred at (gu) : 74.91314 91.13937 90.05867 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 50665 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28618 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 13926 mr = 30380 m= 1306 mr = 8363 m= 36 mr = 454 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 679 time to turn everything in is 0.4400000 number of dielectric boundary points 26736 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 333 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 18479 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) : 0.5174795 object centre at (A) : 50.07850 65.38800 -1.066500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.6930840E-03 2.5092810E-03 midg,1,midg; midg,igrid,midg -2.0260958E-03 -8.2608499E-04 1,midg,midg; igrid,midg,midg 1.7863022E-03 -1.6297754E-02 gauss-seidel spectral radius is 0.9979475 estimated iterations to convergence 176 setup time was (sec) 0.7700000 now iterating at: 08:20:48 rms-change max change #iterations 2.704019 129.1333 at 10iterations 1.052123 48.01826 at 20iterations 0.4127571 20.52754 at 30iterations 0.1627085 6.699985 at 40iterations 6.3653164E-02 2.725141 at 50iterations 2.4989503E-02 1.073912 at 60iterations 9.8931575E-03 0.4352427 at 70iterations 3.9549558E-03 0.1696167 at 80iterations 1.6407334E-03 7.1346283E-02 at 90iterations 7.2484883E-04 3.2768250E-02 at 100iterations 3.6217415E-04 1.6806602E-02 at 110iterations 2.0506649E-04 9.9678040E-03 at 120iterations finished qdiffx linear iterations at : 08:20:58 total time elapsed so far: 11.14000 # loops : 120 mean,max change (kT/e) : 2.0506649E-04 9.9678040E-03 energy calculations done at 11.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.32000 DelPhi exited at 08:20:59 11.322u 0.437s 0:12.32 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 Tue Oct 11 2011 at 08:20:59 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 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: 2.328658 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): 15.68100 84.47600 ymin,ymax (A): 37.45400 93.32200 zmin,zma (A): -25.63000 23.49700 x,y,z range (A): 68.79500 55.86800 49.12700 scale (grids/A): 2.328658 object centre (A): 50.07850 65.38800 -1.066500 number of atom coordinates read : 2581 total number of charged atoms : 2442 net assigned charge : -0.9999892 assigned positive charge : 383.5807 centred at (gu) : 66.96352 91.84421 89.85973 assigned negative charge : -384.5815 centred at (gu) : 67.36960 91.70903 90.08780 start vw surface at 0.1300000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 117639 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28618 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 48421 mr = 75806 m= 12736 mr = 35124 m= 1727 mr = 8553 m= 96 mr = 885 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 2200 time to turn everything in is 1.060000 number of dielectric boundary points 60233 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 41 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 19493 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) : 1.552438 object centre at (A) : 50.07850 65.38800 -1.066500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1193944 4.8676245E-02 midg,1,midg; midg,igrid,midg -8.0028605E-03 2.3047689E-02 1,midg,midg; igrid,midg,midg 0.1273933 -0.3817485 gauss-seidel spectral radius is 0.9990520 estimated iterations to convergence 257 setup time was (sec) 1.390000 now iterating at: 08:21:01 rms-change max change #iterations 7.512536 312.1014 at 10iterations 4.207523 142.4877 at 20iterations 2.320479 66.09566 at 30iterations 1.267989 36.15656 at 40iterations 0.6894468 17.58482 at 50iterations 0.3738573 9.968792 at 60iterations 0.2022743 5.457271 at 70iterations 0.1088489 2.882065 at 80iterations 5.8373932E-02 1.483253 at 90iterations 3.1360894E-02 0.7684135 at 100iterations 1.6851569E-02 0.4066715 at 110iterations 9.0742717E-03 0.2256107 at 120iterations 4.8619648E-03 0.1219368 at 130iterations 2.6225676E-03 5.9173584E-02 at 140iterations 1.4325548E-03 3.9867401E-02 at 150iterations 7.9633098E-04 1.9251823E-02 at 160iterations 4.5793204E-04 1.2078285E-02 at 170iterations 2.7784752E-04 8.1291199E-03 at 180iterations finished qdiffx linear iterations at : 08:21:17 total time elapsed so far: 17.42000 # loops : 180 mean,max change (kT/e) : 2.7784752E-04 8.1291199E-03 energy calculations done at 17.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.60000 DelPhi exited at 08:21:17 17.603u 0.438s 0:18.64 96.7% 0+0k 0+0io 0pf+0w