Sun Oct 9 19:43:17 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 Sun Oct 9 2011 at 19:43:17 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: 347 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5305 !!! WARNING: HIR 341 has a net charge of 0.5140 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5181498 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): 3.277000 68.35300 ymin,ymax (A): -8.944000 52.29000 zmin,zma (A): -1.704000 67.00200 x,y,z range (A): 65.07600 61.23400 68.70600 scale (grids/A): 0.5181498 object centre (A): 35.81500 21.67300 32.64900 number of atom coordinates read : 5305 total number of charged atoms : 5138 net assigned charge : 6.558045 assigned positive charge : 818.7714 centred at (gu) : 88.16904 89.69351 88.78708 assigned negative charge : -812.2196 centred at (gu) : 88.05129 89.71152 88.70489 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 9129 nv = 96 ne = 84 npr = 107569 no. pairs analyzed = 107569 no. exposed pairs = 6091 no. arc points = 41772 no. surface atoms = 2072 nbur = 3233 mkacc time = 0.2500000 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= 328 mr = 5146 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 4299 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4183 ## 574 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 12229 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6667540E-10 3.4386860E-10 midg,1,midg; midg,igrid,midg 2.3336713E-10 6.5598214E-11 1,midg,midg; igrid,midg,midg -5.5641036E-10 3.8003473E-10 gauss-seidel spectral radius is 0.9809797 estimated iterations to convergence 60 setup time was (sec) 0.7200000 now iterating at: 19:43:18 rms-change max change #iterations 8.2129695E-02 11.66094 at 10iterations 9.3190027E-03 1.486881 at 20iterations 3.3666193E-03 0.5452271 at 30iterations 1.4070815E-03 0.2305794 at 40iterations 5.9355499E-04 9.6946716E-02 at 50iterations finished qdiffx linear iterations at : 19:43:20 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 5.9355499E-04 9.6946716E-02 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 19:43:21 3.519u 0.175s 0:03.99 92.2% 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 Sun Oct 9 2011 at 19:43:21 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: 347 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5305 !!! WARNING: HIR 341 has a net charge of 0.5140 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.554449 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): 3.277000 68.35300 ymin,ymax (A): -8.944000 52.29000 zmin,zma (A): -1.704000 67.00200 x,y,z range (A): 65.07600 61.23400 68.70600 scale (grids/A): 1.554449 object centre (A): 35.81500 21.67300 32.64900 number of atom coordinates read : 5305 total number of charged atoms : 5138 net assigned charge : 6.558045 assigned positive charge : 818.7714 centred at (gu) : 84.50578 89.07898 86.35989 assigned negative charge : -812.2196 centred at (gu) : 84.15396 89.13431 86.11474 start vw surface at 0.2300000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 104105 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41772 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 33404 mr = 75414 m= 3155 mr = 23550 m= 68 mr = 1474 m= 0 mr = 10 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7600000 number of dielectric boundary points 40284 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 545 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 38810 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) : 0.5181498 object centre at (A) : 35.81500 21.67300 32.64900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7107651E-02 2.6630946E-02 midg,1,midg; midg,igrid,midg 1.4811884E-02 6.0718125E-03 1,midg,midg; igrid,midg,midg -1.1208477E-02 1.2012597E-02 gauss-seidel spectral radius is 0.9982071 estimated iterations to convergence 188 setup time was (sec) 1.050000 now iterating at: 19:43:22 rms-change max change #iterations 4.239546 149.6913 at 10iterations 1.777051 57.63215 at 20iterations 0.7490964 21.92692 at 30iterations 0.3149424 9.237234 at 40iterations 0.1332351 4.359547 at 50iterations 5.7278346E-02 1.746651 at 60iterations 2.5432106E-02 0.7811966 at 70iterations 1.2415006E-02 0.4253387 at 80iterations 6.9956128E-03 0.2499466 at 90iterations 4.4980543E-03 0.1482315 at 100iterations 3.1537218E-03 0.1038780 at 110iterations 2.2936133E-03 7.5408936E-02 at 120iterations finished qdiffx linear iterations at : 19:43:28 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 2.2936133E-03 7.5408936E-02 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 19:43:29 7.760u 0.159s 0:08.19 96.5% 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 Sun Oct 9 2011 at 19:43:29 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: 347 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5305 !!! WARNING: HIR 341 has a net charge of 0.5140 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.331674 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): 3.277000 68.35300 ymin,ymax (A): -8.944000 52.29000 zmin,zma (A): -1.704000 67.00200 x,y,z range (A): 65.07600 61.23400 68.70600 scale (grids/A): 2.331674 object centre (A): 35.81500 21.67300 32.64900 number of atom coordinates read : 5305 total number of charged atoms : 5138 net assigned charge : 6.558045 assigned positive charge : 818.7714 centred at (gu) : 81.75827 88.61819 84.53955 assigned negative charge : -812.2196 centred at (gu) : 81.23091 88.70135 84.17202 start vw surface at 0.2200000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 242686 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41772 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 116997 mr = 184049 m= 32461 mr = 94674 m= 4896 mr = 24434 m= 306 mr = 3170 m= 4 mr = 145 m= 0 mr = 0 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.860000 number of dielectric boundary points 90878 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 47 iepsmp to db, and charging done at 2.010000 number of grid points assigned charge 40990 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) : 1.554449 object centre at (A) : 35.81500 21.67300 32.64900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3644764 0.8008575 midg,1,midg; midg,igrid,midg 0.2204507 5.4389812E-02 1,midg,midg; igrid,midg,midg -0.3512826 0.1844306 gauss-seidel spectral radius is 0.9991896 estimated iterations to convergence 277 setup time was (sec) 2.240000 now iterating at: 19:43:31 rms-change max change #iterations 11.21952 312.3361 at 10iterations 6.451984 145.6537 at 20iterations 3.675954 76.87291 at 30iterations 2.087280 42.22256 at 40iterations 1.183538 21.59241 at 50iterations 0.6689200 12.12428 at 60iterations 0.3776503 6.765958 at 70iterations 0.2128844 3.834314 at 80iterations 0.1202317 2.170506 at 90iterations 6.8117976E-02 1.160301 at 100iterations 3.8865678E-02 0.6499276 at 110iterations 2.2502169E-02 0.3982697 at 120iterations 1.3458575E-02 0.2575073 at 130iterations 8.4408512E-03 0.1597786 at 140iterations 5.6325868E-03 0.1221542 at 150iterations 4.0385243E-03 8.4529877E-02 at 160iterations 3.0711733E-03 6.4355850E-02 at 170iterations 2.4246629E-03 4.7950745E-02 at 180iterations finished qdiffx linear iterations at : 19:43:42 total time elapsed so far: 12.73000 # loops : 180 mean,max change (kT/e) : 2.4246629E-03 4.7950745E-02 energy calculations done at 12.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.95000 DelPhi exited at 19:43:42 12.948u 0.181s 0:13.49 97.2% 0+0k 0+0io 0pf+0w