Tue Oct 11 07:33:30 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 07:33:30 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3239 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5927801 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): 0.2609999 49.12400 ymin,ymax (A): -8.408999 49.36400 zmin,zma (A): 1.078000 61.13400 x,y,z range (A): 48.86300 57.77300 60.05600 scale (grids/A): 0.5927801 object centre (A): 24.69250 20.47750 31.10600 number of atom coordinates read : 3239 total number of charged atoms : 3074 net assigned charge : -3.099990 assigned positive charge : 482.9698 centred at (gu) : 89.58722 89.44344 90.73441 assigned negative charge : -486.0709 centred at (gu) : 89.54800 89.37796 90.66930 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7452 nv = 96 ne = 84 npr = 66876 no. pairs analyzed = 66876 no. exposed pairs = 3850 no. arc points = 26433 no. surface atoms = 1300 nbur = 1939 mkacc time = 0.1500000 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 = 1.456000 m= 382 mr = 4301 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 75 time to turn everything in is 0.3400000 number of dielectric boundary points 3500 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2548 ## 246 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9357 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.9002258E-09 1.5683047E-09 midg,1,midg; midg,igrid,midg -3.9188430E-09 1.1571216E-09 1,midg,midg; igrid,midg,midg -2.7237064E-09 3.3987535E-10 gauss-seidel spectral radius is 0.9853224 estimated iterations to convergence 68 setup time was (sec) 0.5500000 now iterating at: 07:33:31 rms-change max change #iterations 0.1163415 20.70984 at 10iterations 1.0547571E-02 1.485416 at 20iterations 1.2937189E-03 0.1930313 at 30iterations 3.0999453E-04 5.0401688E-02 at 40iterations 8.7917710E-05 1.4562607E-02 at 50iterations finished qdiffx linear iterations at : 07:33:33 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 8.7917710E-05 1.4562607E-02 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 07:33:34 3.139u 0.146s 0:03.64 89.8% 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 07:33:34 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3239 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.778340 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): 0.2609999 49.12400 ymin,ymax (A): -8.408999 49.36400 zmin,zma (A): 1.078000 61.13400 x,y,z range (A): 48.86300 57.77300 60.05600 scale (grids/A): 1.778340 object centre (A): 24.69250 20.47750 31.10600 number of atom coordinates read : 3239 total number of charged atoms : 3074 net assigned charge : -3.099990 assigned positive charge : 482.9698 centred at (gu) : 88.76081 88.32922 92.20260 assigned negative charge : -486.0709 centred at (gu) : 88.64364 88.13339 92.00726 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 82045 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26433 grid for indexing accessible points = 1.400000 m= 29744 mr = 58635 m= 4010 mr = 22532 m= 158 mr = 2493 m= 0 mr = 46 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 2384 time to turn everything in is 0.5700000 number of dielectric boundary points 32251 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 201 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 23915 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) : 0.5927801 object centre at (A) : 24.69250 20.47750 31.10600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5414125E-02 1.3247626E-03 midg,1,midg; midg,igrid,midg -1.8874731E-02 7.4386438E-03 1,midg,midg; igrid,midg,midg -1.4260435E-02 -4.7484664E-03 gauss-seidel spectral radius is 0.9984996 estimated iterations to convergence 205 setup time was (sec) 0.8600000 now iterating at: 07:33:35 rms-change max change #iterations 4.185229 177.1996 at 10iterations 1.886091 67.82522 at 20iterations 0.8542857 26.60792 at 30iterations 0.3873937 12.50855 at 40iterations 0.1755862 5.134508 at 50iterations 7.9724923E-02 2.860346 at 60iterations 3.6129892E-02 1.140457 at 70iterations 1.6405128E-02 0.5281029 at 80iterations 7.4598608E-03 0.2579856 at 90iterations 3.4443650E-03 0.1145020 at 100iterations 1.6165026E-03 5.5291176E-02 at 110iterations 7.7234936E-04 2.4623871E-02 at 120iterations finished qdiffx linear iterations at : 07:33:41 total time elapsed so far: 7.170000 # loops : 120 mean,max change (kT/e) : 7.7234936E-04 2.4623871E-02 energy calculations done at 7.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.350000 DelPhi exited at 07:33:42 7.356u 0.175s 0:08.39 89.6% 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 07:33:42 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3239 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.667510 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): 0.2609999 49.12400 ymin,ymax (A): -8.408999 49.36400 zmin,zma (A): 1.078000 61.13400 x,y,z range (A): 48.86300 57.77300 60.05600 scale (grids/A): 2.667510 object centre (A): 24.69250 20.47750 31.10600 number of atom coordinates read : 3239 total number of charged atoms : 3074 net assigned charge : -3.099990 assigned positive charge : 482.9698 centred at (gu) : 88.14080 87.49369 93.30376 assigned negative charge : -486.0709 centred at (gu) : 87.96537 87.19979 93.01083 start vw surface at 0.1600000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 190236 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26433 grid for indexing accessible points = 1.400000 m= 98034 mr = 142031 m= 33652 mr = 81763 m= 6899 mr = 27455 m= 787 mr = 5162 m= 41 mr = 505 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 7889 time to turn everything in is 1.440000 number of dielectric boundary points 72729 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 24580 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) : 1.778340 object centre at (A) : 24.69250 20.47750 31.10600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3880143 -0.2310934 midg,1,midg; midg,igrid,midg -0.3641594 0.1044882 1,midg,midg; igrid,midg,midg -0.1581185 -6.2716767E-02 gauss-seidel spectral radius is 0.9992304 estimated iterations to convergence 285 setup time was (sec) 1.760000 now iterating at: 07:33:44 rms-change max change #iterations 10.14648 280.4394 at 10iterations 5.838346 154.5388 at 20iterations 3.348380 70.01301 at 30iterations 1.913002 37.90900 at 40iterations 1.092283 22.29398 at 50iterations 0.6241944 11.58830 at 60iterations 0.3551546 7.737309 at 70iterations 0.2026053 4.058371 at 80iterations 0.1153308 2.653478 at 90iterations 6.5682285E-02 1.281656 at 100iterations 3.7410229E-02 0.6259031 at 110iterations 2.1274695E-02 0.3932743 at 120iterations 1.2129583E-02 0.2205467 at 130iterations 6.9491044E-03 0.1259270 at 140iterations 3.9840373E-03 7.5135231E-02 at 150iterations 2.3107228E-03 4.0973663E-02 at 160iterations 1.3558561E-03 2.4463654E-02 at 170iterations 8.1345683E-04 1.4861107E-02 at 180iterations finished qdiffx linear iterations at : 07:33:55 total time elapsed so far: 12.19000 # loops : 180 mean,max change (kT/e) : 8.1345683E-04 1.4861107E-02 energy calculations done at 12.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.36000 DelPhi exited at 07:33:55 12.366u 0.266s 0:12.93 97.6% 0+0k 0+0io 0pf+0w