Wed Feb 15 08:57:07 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:57:07 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 ! Automatically converted by prot2crg.py # of charge parameter records: 968 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3133 !!! WARNING: ADP 901 has a net charge of -2.0000 !!! WARNING: MG1 902 has a net charge of 2.0000 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: 0.5690265 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): -36.33800 21.65500 ymin,ymax (A): 39.28800 88.26900 zmin,zma (A): -3.904000 58.65900 x,y,z range (A): 57.99300 48.98100 62.56300 scale (grids/A): 0.5690265 object centre (A): -7.341500 63.77850 27.37750 number of atom coordinates read : 3133 total number of charged atoms : 2986 net assigned charge : -3.999984 assigned positive charge : 479.4707 centred at (gu) : 92.12347 89.98642 89.22987 assigned negative charge : -483.4717 centred at (gu) : 92.05611 90.02898 89.19134 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6468 nv = 96 ne = 84 npr = 64412 no. pairs analyzed = 64412 no. exposed pairs = 4189 no. arc points = 28373 no. surface atoms = 1409 nbur = 1724 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 = 1.484000 m= 252 mr = 3239 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.3600000 number of dielectric boundary points 3474 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2930 ## 328 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8504 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4964360E-09 1.2942367E-11 midg,1,midg; midg,igrid,midg 8.6710278E-11 -1.3081438E-09 1,midg,midg; igrid,midg,midg -1.0463531E-09 8.4830581E-10 gauss-seidel spectral radius is 0.9840752 estimated iterations to convergence 65 setup time was (sec) 0.6100000 now iterating at: 08:57:08 rms-change max change #iterations 8.9893125E-02 14.02602 at 10iterations 6.6064610E-03 1.007706 at 20iterations 5.1040435E-04 9.0517044E-02 at 30iterations 5.3374639E-05 9.5767975E-03 at 40iterations 1.1392142E-05 2.4213791E-03 at 50iterations finished qdiffx linear iterations at : 08:57:11 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 1.1392142E-05 2.4213791E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 08:57:11 3.515u 0.167s 0:04.03 91.0% 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 Wed Feb 15 2012 at 08:57:11 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 ! Automatically converted by prot2crg.py # of charge parameter records: 968 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3133 !!! WARNING: ADP 901 has a net charge of -2.0000 !!! WARNING: MG1 902 has a net charge of 2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.707079 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): -36.33800 21.65500 ymin,ymax (A): 39.28800 88.26900 zmin,zma (A): -3.904000 58.65900 x,y,z range (A): 57.99300 48.98100 62.56300 scale (grids/A): 1.707079 object centre (A): -7.341500 63.77850 27.37750 number of atom coordinates read : 3133 total number of charged atoms : 2986 net assigned charge : -3.999984 assigned positive charge : 479.4707 centred at (gu) : 96.36942 89.95861 87.68874 assigned negative charge : -483.4717 centred at (gu) : 96.16797 90.08625 87.57349 start vw surface at 0.1900000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 71243 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28373 grid for indexing accessible points = 1.400000 m= 21992 mr = 47409 m= 2444 mr = 14945 m= 73 mr = 1144 m= 0 mr = 2 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 683 time to turn everything in is 0.5600000 number of dielectric boundary points 32252 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 254 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 23100 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) : 0.5690265 object centre at (A) : -7.341500 63.77850 27.37750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4798155E-04 -3.8096059E-02 midg,1,midg; midg,igrid,midg -7.1255461E-04 -4.1862959E-03 1,midg,midg; igrid,midg,midg -1.2717029E-02 -3.5669245E-03 gauss-seidel spectral radius is 0.9983553 estimated iterations to convergence 196 setup time was (sec) 0.8700000 now iterating at: 08:57:12 rms-change max change #iterations 3.854950 195.4102 at 10iterations 1.665705 57.57737 at 20iterations 0.7248337 23.25832 at 30iterations 0.3156536 11.85995 at 40iterations 0.1370545 4.886746 at 50iterations 5.9606835E-02 2.012546 at 60iterations 2.5899362E-02 0.8400345 at 70iterations 1.1267155E-02 0.3537312 at 80iterations 4.9121985E-03 0.1712780 at 90iterations 2.1310670E-03 7.7281952E-02 at 100iterations 9.2780218E-04 3.0112743E-02 at 110iterations 4.0867506E-04 1.4536381E-02 at 120iterations finished qdiffx linear iterations at : 08:57:19 total time elapsed so far: 7.500000 # loops : 120 mean,max change (kT/e) : 4.0867506E-04 1.4536381E-02 energy calculations done at 7.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 08:57:20 7.702u 0.247s 0:08.46 93.8% 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 Wed Feb 15 2012 at 08:57:20 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 ! Automatically converted by prot2crg.py # of charge parameter records: 968 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3133 !!! WARNING: ADP 901 has a net charge of -2.0000 !!! WARNING: MG1 902 has a net charge of 2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.560619 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): -36.33800 21.65500 ymin,ymax (A): 39.28800 88.26900 zmin,zma (A): -3.904000 58.65900 x,y,z range (A): 57.99300 48.98100 62.56300 scale (grids/A): 2.560619 object centre (A): -7.341500 63.77850 27.37750 number of atom coordinates read : 3133 total number of charged atoms : 2986 net assigned charge : -3.999984 assigned positive charge : 479.4707 centred at (gu) : 99.55396 89.93797 86.53277 assigned negative charge : -483.4717 centred at (gu) : 99.25200 90.12927 86.36003 start vw surface at 0.1800000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 165539 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28373 grid for indexing accessible points = 1.400000 m= 75532 mr = 116893 m= 22335 mr = 58737 m= 3878 mr = 16690 m= 324 mr = 2453 m= 7 mr = 129 m= 0 mr = 2 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 2342 time to turn everything in is 1.290000 number of dielectric boundary points 72711 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 23882 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) : 1.707079 object centre at (A) : -7.341500 63.77850 27.37750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0455191E-02 -0.7853033 midg,1,midg; midg,igrid,midg -6.1849426E-03 -6.2536314E-02 1,midg,midg; igrid,midg,midg -0.1395256 1.0272485E-02 gauss-seidel spectral radius is 0.9991914 estimated iterations to convergence 278 setup time was (sec) 1.570000 now iterating at: 08:57:21 rms-change max change #iterations 9.662391 331.1634 at 10iterations 5.510985 143.9423 at 20iterations 3.111167 76.67912 at 30iterations 1.759899 38.63928 at 40iterations 0.9933810 21.28060 at 50iterations 0.5590492 12.34056 at 60iterations 0.3136190 6.575031 at 70iterations 0.1762679 3.451591 at 80iterations 9.9066615E-02 2.105614 at 90iterations 5.5445928E-02 1.088339 at 100iterations 3.1144734E-02 0.6768351 at 110iterations 1.7428020E-02 0.3482151 at 120iterations 9.7749187E-03 0.1803594 at 130iterations 5.4734037E-03 9.5993042E-02 at 140iterations 3.0757086E-03 6.5741539E-02 at 150iterations 1.7255016E-03 3.3742428E-02 at 160iterations 9.7565370E-04 2.0195007E-02 at 170iterations 5.5525487E-04 1.2063980E-02 at 180iterations finished qdiffx linear iterations at : 08:57:32 total time elapsed so far: 12.17000 # loops : 180 mean,max change (kT/e) : 5.5525487E-04 1.2063980E-02 energy calculations done at 12.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.37000 DelPhi exited at 08:57:33 12.368u 0.226s 0:12.89 97.5% 0+0k 0+0io 0pf+0w