Sat Oct 15 15:26:50 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+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 Sat Oct 15 2011 at 15:26:50 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2990 !!! WARNING: GLM 77 has a net charge of -0.1880 !!! WARNING: HIZ 119 has a net charge of 0.2000 !!! WARNING: ZN8 849 has a net charge of 1.4000 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: 0.6171983 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): 101.8300 159.1170 ymin,ymax (A): 54.85600 107.9080 zmin,zma (A): -58.23500 -0.5549999 x,y,z range (A): 57.28700 53.05201 57.68000 scale (grids/A): 0.6171983 object centre (A): 130.4735 81.38200 -29.39500 number of atom coordinates read : 2990 total number of charged atoms : 2831 net assigned charge : 7.412017 assigned positive charge : 455.3671 centred at (gu) : 90.84053 89.56618 90.33323 assigned negative charge : -447.9560 centred at (gu) : 91.02515 89.75443 90.49319 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7539 nv = 96 ne = 84 npr = 60044 no. pairs analyzed = 60044 no. exposed pairs = 3700 no. arc points = 25873 no. surface atoms = 1248 nbur = 1742 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 366 mr = 4149 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3800000 number of dielectric boundary points 3723 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2570 ## 282 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9281 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5522103E-08 -6.3820558E-09 midg,1,midg; midg,igrid,midg 2.0517856E-08 -7.2069573E-09 1,midg,midg; igrid,midg,midg 1.5271747E-08 -9.3953734E-09 gauss-seidel spectral radius is 0.9864382 estimated iterations to convergence 70 setup time was (sec) 0.6800000 now iterating at: 15:26:51 rms-change max change #iterations 0.1324674 19.56562 at 10iterations 1.2118281E-02 1.929943 at 20iterations 1.1369135E-03 0.1538911 at 30iterations 1.5047072E-04 2.1673203E-02 at 40iterations 4.3811888E-05 6.7100525E-03 at 50iterations finished qdiffx linear iterations at : 15:26:56 total time elapsed so far: 5.090000 # loops : 50 mean,max change (kT/e) : 4.3811888E-05 6.7100525E-03 energy calculations done at 5.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.250000 DelPhi exited at 15:26:56 5.251u 0.474s 0:06.05 94.5% 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 Sat Oct 15 2011 at 15:26:56 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2990 !!! WARNING: GLM 77 has a net charge of -0.1880 !!! WARNING: HIZ 119 has a net charge of 0.2000 !!! WARNING: ZN8 849 has a net charge of 1.4000 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: 1.851595 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): 101.8300 159.1170 ymin,ymax (A): 54.85600 107.9080 zmin,zma (A): -58.23500 -0.5549999 x,y,z range (A): 57.28700 53.05201 57.68000 scale (grids/A): 1.851595 object centre (A): 130.4735 81.38200 -29.39500 number of atom coordinates read : 2990 total number of charged atoms : 2831 net assigned charge : 7.412017 assigned positive charge : 455.3671 centred at (gu) : 92.52092 88.69781 90.99915 assigned negative charge : -447.9560 centred at (gu) : 93.07494 89.26254 91.47923 start vw surface at 0.1200000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 81335 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25873 grid for indexing accessible points = 1.400000 m= 28221 mr = 56415 m= 3960 mr = 20645 m= 162 mr = 2316 m= 0 mr = 27 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 2040 time to turn everything in is 0.6800000 number of dielectric boundary points 34275 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 215 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 22181 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) : 0.6171983 object centre at (A) : 130.4735 81.38200 -29.39500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4255035E-02 -6.2976326E-03 midg,1,midg; midg,igrid,midg 3.7133810E-03 -1.7085571E-02 1,midg,midg; igrid,midg,midg 6.7853853E-02 -4.7885771E-03 gauss-seidel spectral radius is 0.9986007 estimated iterations to convergence 212 setup time was (sec) 1.070000 now iterating at: 15:26:58 rms-change max change #iterations 4.364697 166.9589 at 10iterations 2.019357 69.06173 at 20iterations 0.9413632 33.30017 at 30iterations 0.4363412 15.01809 at 40iterations 0.2035738 6.817060 at 50iterations 9.4324641E-02 3.015774 at 60iterations 4.3899350E-02 1.312916 at 70iterations 2.0378157E-02 0.6591187 at 80iterations 9.4862487E-03 0.2952957 at 90iterations 4.4177771E-03 0.1316872 at 100iterations 2.0600744E-03 6.3404083E-02 at 110iterations 9.6733862E-04 3.1891584E-02 at 120iterations finished qdiffx linear iterations at : 15:27:11 total time elapsed so far: 12.69000 # loops : 120 mean,max change (kT/e) : 9.6733862E-04 3.1891584E-02 energy calculations done at 12.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.86000 DelPhi exited at 15:27:11 12.866u 0.561s 0:15.15 88.5% 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 Sat Oct 15 2011 at 15:27:12 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2990 !!! WARNING: GLM 77 has a net charge of -0.1880 !!! WARNING: HIZ 119 has a net charge of 0.2000 !!! WARNING: ZN8 849 has a net charge of 1.4000 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: 2.777392 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): 101.8300 159.1170 ymin,ymax (A): 54.85600 107.9080 zmin,zma (A): -58.23500 -0.5549999 x,y,z range (A): 57.28700 53.05201 57.68000 scale (grids/A): 2.777392 object centre (A): 130.4735 81.38200 -29.39500 number of atom coordinates read : 2990 total number of charged atoms : 2831 net assigned charge : 7.412017 assigned positive charge : 455.3671 centred at (gu) : 93.78110 88.04655 91.49857 assigned negative charge : -447.9560 centred at (gu) : 94.61220 88.89373 92.21877 start vw surface at 0.1300000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 188394 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25873 grid for indexing accessible points = 1.400000 m= 93280 mr = 137199 m= 31509 mr = 75946 m= 6858 mr = 24928 m= 793 mr = 4962 m= 32 mr = 464 m= 0 mr = 12 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 6672 time to turn everything in is 1.790000 number of dielectric boundary points 77355 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 22646 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) : 1.851595 object centre at (A) : 130.4735 81.38200 -29.39500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5400258 5.5202436E-02 midg,1,midg; midg,igrid,midg -7.0674606E-02 -0.1476901 1,midg,midg; igrid,midg,midg 0.9114205 -0.1152107 gauss-seidel spectral radius is 0.9992546 estimated iterations to convergence 289 setup time was (sec) 2.190000 now iterating at: 15:27:17 rms-change max change #iterations 10.36867 381.7476 at 10iterations 6.106399 128.9156 at 20iterations 3.561680 76.53003 at 30iterations 2.073609 38.78870 at 40iterations 1.202346 23.28043 at 50iterations 0.6960893 15.73766 at 60iterations 0.4034773 7.259064 at 70iterations 0.2331903 4.159340 at 80iterations 0.1343683 2.479342 at 90iterations 7.7549241E-02 1.376575 at 100iterations 4.4641264E-02 0.7846975 at 110iterations 2.5649196E-02 0.4402852 at 120iterations 1.4768941E-02 0.2670827 at 130iterations 8.5035702E-03 0.1600590 at 140iterations 4.8970808E-03 8.5441589E-02 at 150iterations 2.8238052E-03 4.8513412E-02 at 160iterations 1.6337576E-03 2.8834343E-02 at 170iterations 9.5152261E-04 1.7303467E-02 at 180iterations finished qdiffx linear iterations at : 15:27:49 total time elapsed so far: 23.32000 # loops : 180 mean,max change (kT/e) : 9.5152261E-04 1.7303467E-02 energy calculations done at 23.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.49000 DelPhi exited at 15:27:50 23.494u 0.568s 0:38.03 63.2% 0+0k 0+0io 0pf+0w