Tue Oct 11 03:19:41 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+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 03:19:41 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2637 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: 0.5403108 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): -12.31200 46.52800 ymin,ymax (A): -8.634000 36.09700 zmin,zma (A): -35.94100 29.94700 x,y,z range (A): 58.84000 44.73100 65.88800 scale (grids/A): 0.5403108 object centre (A): 17.10800 13.73150 -2.997001 number of atom coordinates read : 2637 total number of charged atoms : 2491 net assigned charge : 3.500013 assigned positive charge : 391.3857 centred at (gu) : 88.74417 90.63223 91.48145 assigned negative charge : -387.8865 centred at (gu) : 88.81993 90.57730 91.41965 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5191 nv = 96 ne = 84 npr = 50752 no. pairs analyzed = 50752 no. exposed pairs = 3795 no. arc points = 28259 no. surface atoms = 1259 nbur = 1378 mkacc time = 9.0000004E-02 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 = 1.596000 m= 197 mr = 2296 m= 0 mr = 6 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3086 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2748 ## 388 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 6653 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.6241327E-11 6.5036015E-10 midg,1,midg; midg,igrid,midg -8.0462713E-11 4.8753218E-10 1,midg,midg; igrid,midg,midg 7.0228195E-10 -1.3976631E-10 gauss-seidel spectral radius is 0.9823344 estimated iterations to convergence 62 setup time was (sec) 0.3800000 now iterating at: 03:19:41 rms-change max change #iterations 6.7164846E-02 13.60110 at 10iterations 4.2653051E-03 0.8099918 at 20iterations 2.6757782E-04 4.8965454E-02 at 30iterations 1.7459459E-05 3.5638809E-03 at 40iterations 1.1578509E-06 2.5558472E-04 at 50iterations finished qdiffx linear iterations at : 03:19:44 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.1578509E-06 2.5558472E-04 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 03:19:45 3.425u 0.185s 0:04.03 89.3% 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 03:19:45 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2637 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: 1.620932 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): -12.31200 46.52800 ymin,ymax (A): -8.634000 36.09700 zmin,zma (A): -35.94100 29.94700 x,y,z range (A): 58.84000 44.73100 65.88800 scale (grids/A): 1.620932 object centre (A): 17.10800 13.73150 -2.997001 number of atom coordinates read : 2637 total number of charged atoms : 2491 net assigned charge : 3.500013 assigned positive charge : 391.3857 centred at (gu) : 86.23205 91.89608 94.44363 assigned negative charge : -387.8865 centred at (gu) : 86.45949 91.73175 94.25880 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 56463 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28259 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 15713 mr = 34632 m= 1456 mr = 9846 m= 51 mr = 547 m= 0 mr = 2 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 308 time to turn everything in is 0.3000000 number of dielectric boundary points 28656 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 318 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 19058 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) : 0.5403108 object centre at (A) : 17.10800 13.73150 -2.997001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0198848E-02 2.0569935E-02 midg,1,midg; midg,igrid,midg -2.4280550E-03 2.8109862E-03 1,midg,midg; igrid,midg,midg 5.2451589E-03 -3.1691490E-04 gauss-seidel spectral radius is 0.9981349 estimated iterations to convergence 184 setup time was (sec) 0.5100000 now iterating at: 03:19:46 rms-change max change #iterations 3.037314 166.8358 at 10iterations 1.241235 53.55996 at 20iterations 0.5100572 20.62449 at 30iterations 0.2084530 8.463428 at 40iterations 8.5563876E-02 3.199294 at 50iterations 3.5150569E-02 1.307798 at 60iterations 1.4439966E-02 0.5429459 at 70iterations 5.9277578E-03 0.2298203 at 80iterations 2.4279242E-03 9.7183228E-02 at 90iterations 1.0044257E-03 4.1556478E-02 at 100iterations 4.1155005E-04 1.5953064E-02 at 110iterations 1.6989505E-04 7.4138641E-03 at 120iterations finished qdiffx linear iterations at : 03:19:53 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 1.6989505E-04 7.4138641E-03 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.710000 DelPhi exited at 03:19:54 7.710u 0.236s 0:08.54 92.9% 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 03:19:54 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2637 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: 2.431399 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): -12.31200 46.52800 ymin,ymax (A): -8.634000 36.09700 zmin,zma (A): -35.94100 29.94700 x,y,z range (A): 58.84000 44.73100 65.88800 scale (grids/A): 2.431399 object centre (A): 17.10800 13.73150 -2.997001 number of atom coordinates read : 2637 total number of charged atoms : 2491 net assigned charge : 3.500013 assigned positive charge : 391.3857 centred at (gu) : 84.34798 92.84396 96.66554 assigned negative charge : -387.8865 centred at (gu) : 84.68924 92.59753 96.38802 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 130946 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28259 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 54924 mr = 85696 m= 14583 mr = 41113 m= 2104 mr = 10185 m= 137 mr = 1155 m= 3 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 1076 time to turn everything in is 0.6800000 number of dielectric boundary points 64508 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 19902 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) : 1.620932 object centre at (A) : 17.10800 13.73150 -2.997001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3123080 0.2826651 midg,1,midg; midg,igrid,midg -3.1035768E-02 3.4342512E-02 1,midg,midg; igrid,midg,midg 5.0183412E-02 4.5771409E-02 gauss-seidel spectral radius is 0.9991145 estimated iterations to convergence 265 setup time was (sec) 0.9100000 now iterating at: 03:19:55 rms-change max change #iterations 7.955887 294.9185 at 10iterations 4.439504 127.4385 at 20iterations 2.474310 69.86301 at 30iterations 1.364574 34.81837 at 40iterations 0.7483192 18.72675 at 50iterations 0.4118648 9.455461 at 60iterations 0.2250686 5.373202 at 70iterations 0.1231122 3.031418 at 80iterations 6.7287691E-02 1.667528 at 90iterations 3.6662441E-02 0.8597698 at 100iterations 1.9969476E-02 0.4384270 at 110iterations 1.0914647E-02 0.2377778 at 120iterations 5.9187440E-03 0.1303711 at 130iterations 3.2325776E-03 7.6749802E-02 at 140iterations 1.7606834E-03 3.5867691E-02 at 150iterations 9.5784717E-04 2.2935867E-02 at 160iterations 5.2082725E-04 1.1231899E-02 at 170iterations 2.8411770E-04 6.0882568E-03 at 180iterations finished qdiffx linear iterations at : 03:20:06 total time elapsed so far: 12.09000 # loops : 180 mean,max change (kT/e) : 2.8411770E-04 6.0882568E-03 energy calculations done at 12.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.22000 DelPhi exited at 03:20:07 12.222u 0.246s 0:12.98 95.9% 0+0k 0+0io 0pf+0w