Mon Oct 10 13:55:45 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 Mon Oct 10 2011 at 13:55:46 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2335 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: 0.6357256 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): -27.16800 25.59700 ymin,ymax (A): 7.763000 48.70100 zmin,zma (A): -13.09600 42.90300 x,y,z range (A): 52.76500 40.93800 55.99900 scale (grids/A): 0.6357256 object centre (A): -0.7854996 28.23200 14.90350 number of atom coordinates read : 2335 total number of charged atoms : 2201 net assigned charge : 8.000017 assigned positive charge : 337.9166 centred at (gu) : 91.02227 90.98767 91.12844 assigned negative charge : -329.9171 centred at (gu) : 90.93334 90.90626 91.11775 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6371 nv = 96 ne = 84 npr = 47488 no. pairs analyzed = 47488 no. exposed pairs = 3187 no. arc points = 22215 no. surface atoms = 1064 nbur = 1271 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 335 mr = 3209 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3479 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2143 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 7611 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.2551205E-09 1.3970831E-08 midg,1,midg; midg,igrid,midg 2.4025133E-09 2.1219369E-08 1,midg,midg; igrid,midg,midg 1.8491024E-09 2.2190767E-08 gauss-seidel spectral radius is 0.9871647 estimated iterations to convergence 72 setup time was (sec) 0.6500000 now iterating at: 13:55:46 rms-change max change #iterations 0.1288577 21.85440 at 10iterations 1.2466602E-02 2.008671 at 20iterations 1.2520188E-03 0.1948814 at 30iterations 1.2879766E-04 2.0027161E-02 at 40iterations 1.7313139E-05 2.7980804E-03 at 50iterations finished qdiffx linear iterations at : 13:55:50 total time elapsed so far: 3.820000 # loops : 50 mean,max change (kT/e) : 1.7313139E-05 2.7980804E-03 energy calculations done at 3.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.050000 DelPhi exited at 13:55:50 4.057u 0.196s 0:04.58 92.5% 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 Mon Oct 10 2011 at 13:55:50 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2335 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: 1.907177 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): -27.16800 25.59700 ymin,ymax (A): 7.763000 48.70100 zmin,zma (A): -13.09600 42.90300 x,y,z range (A): 52.76500 40.93800 55.99900 scale (grids/A): 1.907177 object centre (A): -0.7854996 28.23200 14.90350 number of atom coordinates read : 2335 total number of charged atoms : 2201 net assigned charge : 8.000017 assigned positive charge : 337.9166 centred at (gu) : 93.06655 92.96281 93.38514 assigned negative charge : -329.9171 centred at (gu) : 92.80025 92.71880 93.35356 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 67719 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22215 grid for indexing accessible points = 1.400000 m= 23190 mr = 44673 m= 3453 mr = 16039 m= 218 mr = 1898 m= 3 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 31926 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 17327 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) : 0.6357256 object centre at (A) : -0.7854996 28.23200 14.90350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1517878E-02 2.7626539E-02 midg,1,midg; midg,igrid,midg -2.3204929E-03 2.2947043E-02 1,midg,midg; igrid,midg,midg 2.8095573E-02 4.7614429E-02 gauss-seidel spectral radius is 0.9986187 estimated iterations to convergence 213 setup time was (sec) 0.9900000 now iterating at: 13:55:51 rms-change max change #iterations 3.900821 184.5447 at 10iterations 1.811473 62.22680 at 20iterations 0.8458512 31.41874 at 30iterations 0.3932513 12.11802 at 40iterations 0.1824419 6.228483 at 50iterations 8.5323207E-02 3.207666 at 60iterations 3.9567009E-02 1.461279 at 70iterations 1.8424597E-02 0.6064596 at 80iterations 8.6038345E-03 0.2781401 at 90iterations 4.0055565E-03 0.1314526 at 100iterations 1.8667232E-03 6.1774731E-02 at 110iterations 8.6809642E-04 3.2334328E-02 at 120iterations finished qdiffx linear iterations at : 13:55:59 total time elapsed so far: 9.000000 # loops : 120 mean,max change (kT/e) : 8.6809642E-04 3.2334328E-02 energy calculations done at 9.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.240000 DelPhi exited at 13:56:00 9.240u 0.215s 0:10.08 93.7% 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 13:56:00 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2335 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: 2.860765 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): -27.16800 25.59700 ymin,ymax (A): 7.763000 48.70100 zmin,zma (A): -13.09600 42.90300 x,y,z range (A): 52.76500 40.93800 55.99900 scale (grids/A): 2.860765 object centre (A): -0.7854996 28.23200 14.90350 number of atom coordinates read : 2335 total number of charged atoms : 2201 net assigned charge : 8.000017 assigned positive charge : 337.9166 centred at (gu) : 94.59977 94.44418 95.07767 assigned negative charge : -329.9171 centred at (gu) : 94.20035 94.07830 95.03043 start vw surface at 0.1800000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 156576 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22215 grid for indexing accessible points = 1.400000 m= 75071 mr = 109064 m= 26233 mr = 59159 m= 5977 mr = 19876 m= 836 mr = 4122 m= 52 mr = 435 m= 0 mr = 15 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.580000 number of dielectric boundary points 72074 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 17606 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) : 1.907177 object centre at (A) : -0.7854996 28.23200 14.90350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7579499 0.3372675 midg,1,midg; midg,igrid,midg -3.2311566E-02 0.2436342 1,midg,midg; igrid,midg,midg 0.3884195 0.4643996 gauss-seidel spectral radius is 0.9992613 estimated iterations to convergence 290 setup time was (sec) 1.960000 now iterating at: 13:56:03 rms-change max change #iterations 9.327286 347.9727 at 10iterations 5.487449 156.6095 at 20iterations 3.215372 74.85443 at 30iterations 1.871205 41.40974 at 40iterations 1.085908 22.48020 at 50iterations 0.6296381 13.43643 at 60iterations 0.3651367 8.274292 at 70iterations 0.2106962 4.032346 at 80iterations 0.1214386 2.674571 at 90iterations 7.0265032E-02 1.471288 at 100iterations 4.0440187E-02 0.7850552 at 110iterations 2.3267236E-02 0.4319382 at 120iterations 1.3428902E-02 0.2572556 at 130iterations 7.7158292E-03 0.1574125 at 140iterations 4.4475468E-03 8.5311890E-02 at 150iterations 2.5603797E-03 5.1631927E-02 at 160iterations 1.4762859E-03 2.8278351E-02 at 170iterations 8.5289724E-04 1.7223358E-02 at 180iterations finished qdiffx linear iterations at : 13:56:15 total time elapsed so far: 14.54000 # loops : 180 mean,max change (kT/e) : 8.5289724E-04 1.7223358E-02 energy calculations done at 14.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.78000 DelPhi exited at 13:56:16 14.783u 0.219s 0:15.33 97.7% 0+0k 0+0io 0pf+0w