Mon Oct 10 14:05:01 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 Mon Oct 10 2011 at 14:05:01 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2277 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6594058 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): -29.78700 22.24800 ymin,ymax (A): 27.59400 70.15500 zmin,zma (A): 14.12500 68.11300 x,y,z range (A): 52.03500 42.56100 53.98800 scale (grids/A): 0.6594058 object centre (A): -3.769500 48.87450 41.11900 number of atom coordinates read : 2277 total number of charged atoms : 2143 net assigned charge : 11.51402 assigned positive charge : 332.9696 centred at (gu) : 91.63573 91.67979 89.18354 assigned negative charge : -321.4562 centred at (gu) : 91.61860 91.59773 89.15242 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6947 nv = 96 ne = 84 npr = 44882 no. pairs analyzed = 44882 no. exposed pairs = 3103 no. arc points = 22412 no. surface atoms = 1033 nbur = 1244 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 473 mr = 3579 m= 2 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3771 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2102 ## 189 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7986 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7482335E-08 2.8289392E-08 midg,1,midg; midg,igrid,midg 1.0998756E-08 5.8585211E-08 1,midg,midg; igrid,midg,midg 1.8547709E-08 4.3411909E-08 gauss-seidel spectral radius is 0.9880636 estimated iterations to convergence 75 setup time was (sec) 0.4700000 now iterating at: 14:05:02 rms-change max change #iterations 0.1499283 23.34192 at 10iterations 1.6222969E-02 2.447037 at 20iterations 1.8081886E-03 0.2726297 at 30iterations 2.5786957E-04 4.5190811E-02 at 40iterations 5.2682899E-05 1.1219025E-02 at 50iterations finished qdiffx linear iterations at : 14:05:04 total time elapsed so far: 2.870000 # loops : 50 mean,max change (kT/e) : 5.2682899E-05 1.1219025E-02 energy calculations done at 2.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 14:05:05 3.083u 0.143s 0:03.80 84.7% 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 Mon Oct 10 2011 at 14:05:05 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2277 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.978217 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): -29.78700 22.24800 ymin,ymax (A): 27.59400 70.15500 zmin,zma (A): 14.12500 68.11300 x,y,z range (A): 52.03500 42.56100 53.98800 scale (grids/A): 1.978217 object centre (A): -3.769500 48.87450 41.11900 number of atom coordinates read : 2277 total number of charged atoms : 2143 net assigned charge : 11.51402 assigned positive charge : 332.9696 centred at (gu) : 94.90707 95.03913 87.55048 assigned negative charge : -321.4562 centred at (gu) : 94.85587 94.79337 87.45739 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 73650 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22412 grid for indexing accessible points = 1.400000 m= 28026 mr = 49022 m= 5206 mr = 20300 m= 425 mr = 3232 m= 6 mr = 197 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 714 time to turn everything in is 0.5100000 number of dielectric boundary points 34562 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 16955 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) : 0.6594058 object centre at (A) : -3.769500 48.87450 41.11900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6550277E-02 5.2285064E-02 midg,1,midg; midg,igrid,midg -2.2483165E-03 3.7215594E-02 1,midg,midg; igrid,midg,midg 4.8434991E-02 3.0089917E-02 gauss-seidel spectral radius is 0.9987127 estimated iterations to convergence 221 setup time was (sec) 0.7700000 now iterating at: 14:05:06 rms-change max change #iterations 4.170456 210.1482 at 10iterations 1.989100 69.23677 at 20iterations 0.9483809 35.64179 at 30iterations 0.4537728 15.99177 at 40iterations 0.2167310 6.388765 at 50iterations 0.1036693 3.353235 at 60iterations 4.9355704E-02 1.633026 at 70iterations 2.3676487E-02 0.7323322 at 80iterations 1.1337106E-02 0.4195366 at 90iterations 5.4408852E-03 0.1792431 at 100iterations 2.6137610E-03 8.0017090E-02 at 110iterations 1.2674186E-03 3.9409637E-02 at 120iterations finished qdiffx linear iterations at : 14:05:13 total time elapsed so far: 7.280000 # loops : 120 mean,max change (kT/e) : 1.2674186E-03 3.9409637E-02 energy calculations done at 7.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 14:05:13 7.459u 0.166s 0:08.04 94.6% 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 Mon Oct 10 2011 at 14:05:13 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2277 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.967326 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): -29.78700 22.24800 ymin,ymax (A): 27.59400 70.15500 zmin,zma (A): 14.12500 68.11300 x,y,z range (A): 52.03500 42.56100 53.98800 scale (grids/A): 2.967326 object centre (A): -3.769500 48.87450 41.11900 number of atom coordinates read : 2277 total number of charged atoms : 2143 net assigned charge : 11.51402 assigned positive charge : 332.9696 centred at (gu) : 97.36054 97.55865 86.32557 assigned negative charge : -321.4562 centred at (gu) : 97.28390 97.19012 86.18602 start vw surface at 0.2100000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 169870 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22412 grid for indexing accessible points = 1.400000 m= 87507 mr = 119257 m= 34622 mr = 70392 m= 9655 mr = 27527 m= 1759 mr = 7212 m= 178 mr = 1229 m= 7 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 2493 time to turn everything in is 1.450000 number of dielectric boundary points 77891 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 17144 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) : 1.978217 object centre at (A) : -3.769500 48.87450 41.11900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6682433 0.4331053 midg,1,midg; midg,igrid,midg -1.7318107E-02 0.3279256 1,midg,midg; igrid,midg,midg 0.6919038 0.2626491 gauss-seidel spectral radius is 0.9992907 estimated iterations to convergence 296 setup time was (sec) 1.740000 now iterating at: 14:05:15 rms-change max change #iterations 9.870338 362.8819 at 10iterations 5.865003 163.7553 at 20iterations 3.485024 78.56125 at 30iterations 2.058925 46.08450 at 40iterations 1.209072 26.02017 at 50iterations 0.7107100 14.00867 at 60iterations 0.4166388 9.313474 at 70iterations 0.2432961 4.975687 at 80iterations 0.1421013 2.584884 at 90iterations 8.2705483E-02 1.558458 at 100iterations 4.8147239E-02 0.9702816 at 110iterations 2.8108336E-02 0.5151613 at 120iterations 1.6362190E-02 0.2990227 at 130iterations 9.5414985E-03 0.1890116 at 140iterations 5.5478523E-03 9.8512650E-02 at 150iterations 3.2329781E-03 5.7872534E-02 at 160iterations 1.8793491E-03 3.1337738E-02 at 170iterations 1.0958210E-03 2.0743370E-02 at 180iterations finished qdiffx linear iterations at : 14:05:24 total time elapsed so far: 11.03000 # loops : 180 mean,max change (kT/e) : 1.0958210E-03 2.0743370E-02 energy calculations done at 11.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.21000 DelPhi exited at 14:05:25 11.214u 0.179s 0:11.69 97.3% 0+0k 0+0io 0pf+0w