Mon Oct 10 14:42:22 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 14:42:23 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2461 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: 0.6100591 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): -8.526000 46.05800 ymin,ymax (A): -25.30500 33.05000 zmin,zma (A): 9.131000 64.27900 x,y,z range (A): 54.58400 58.35500 55.14800 scale (grids/A): 0.6100591 object centre (A): 18.76600 3.872499 36.70500 number of atom coordinates read : 2461 total number of charged atoms : 2316 net assigned charge : -1.999992 assigned positive charge : 365.4571 centred at (gu) : 89.42949 90.76711 89.20305 assigned negative charge : -367.4577 centred at (gu) : 89.27956 90.64520 89.19906 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6042 nv = 96 ne = 84 npr = 49589 no. pairs analyzed = 49589 no. exposed pairs = 3249 no. arc points = 22789 no. surface atoms = 1094 nbur = 1367 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 259 mr = 3105 m= 0 mr = 8 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3188 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2227 ## 243 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7454 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6206236E-09 -8.3328799E-10 midg,1,midg; midg,igrid,midg -5.8656946E-09 5.3323030E-09 1,midg,midg; igrid,midg,midg -9.4779775E-09 5.0338311E-09 gauss-seidel spectral radius is 0.9860803 estimated iterations to convergence 69 setup time was (sec) 0.6100000 now iterating at: 14:42:24 rms-change max change #iterations 0.1126383 16.53266 at 10iterations 9.8047229E-03 1.354304 at 20iterations 8.6599984E-04 0.1303616 at 30iterations 7.6310193E-05 1.3696671E-02 at 40iterations 6.8359222E-06 1.0761023E-03 at 50iterations finished qdiffx linear iterations at : 14:42:27 total time elapsed so far: 4.460000 # loops : 50 mean,max change (kT/e) : 6.8359222E-06 1.0761023E-03 energy calculations done at 4.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.630000 DelPhi exited at 14:42:28 4.635u 0.398s 0:05.67 88.5% 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 14:42:28 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2461 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.830177 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): -8.526000 46.05800 ymin,ymax (A): -25.30500 33.05000 zmin,zma (A): 9.131000 64.27900 x,y,z range (A): 54.58400 58.35500 55.14800 scale (grids/A): 1.830177 object centre (A): 18.76600 3.872499 36.70500 number of atom coordinates read : 2461 total number of charged atoms : 2316 net assigned charge : -1.999992 assigned positive charge : 365.4571 centred at (gu) : 88.28799 92.30106 87.60868 assigned negative charge : -367.4577 centred at (gu) : 87.83860 91.93564 87.59699 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 65655 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22789 grid for indexing accessible points = 1.400000 m= 21533 mr = 43990 m= 2868 mr = 15088 m= 117 mr = 1460 m= 0 mr = 23 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 29612 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 176 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 18159 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) : 0.6100591 object centre at (A) : 18.76600 3.872499 36.70500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.9599605E-02 -6.8456499E-04 midg,1,midg; midg,igrid,midg -6.1916430E-03 1.6180458E-02 1,midg,midg; igrid,midg,midg -7.1759275E-03 1.1769243E-02 gauss-seidel spectral radius is 0.9985024 estimated iterations to convergence 205 setup time was (sec) 0.8600000 now iterating at: 14:42:30 rms-change max change #iterations 3.799694 161.3613 at 10iterations 1.701081 58.80180 at 20iterations 0.7702965 31.57166 at 30iterations 0.3458761 12.20272 at 40iterations 0.1563461 5.015961 at 50iterations 7.0441395E-02 2.447958 at 60iterations 3.1932704E-02 1.060563 at 70iterations 1.4369251E-02 0.4786243 at 80iterations 6.4928182E-03 0.2690659 at 90iterations 2.9337935E-03 0.1017108 at 100iterations 1.3247150E-03 4.6536446E-02 at 110iterations 6.0032128E-04 2.1060944E-02 at 120iterations finished qdiffx linear iterations at : 14:42:39 total time elapsed so far: 10.68000 # loops : 120 mean,max change (kT/e) : 6.0032128E-04 2.1060944E-02 energy calculations done at 10.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.84000 DelPhi exited at 14:42:40 10.847u 0.464s 0:11.79 95.8% 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 Mon Oct 10 2011 at 14:42:40 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2461 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.745266 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): -8.526000 46.05800 ymin,ymax (A): -25.30500 33.05000 zmin,zma (A): 9.131000 64.27900 x,y,z range (A): 54.58400 58.35500 55.14800 scale (grids/A): 2.745266 object centre (A): 18.76600 3.872499 36.70500 number of atom coordinates read : 2461 total number of charged atoms : 2316 net assigned charge : -1.999992 assigned positive charge : 365.4571 centred at (gu) : 87.43190 93.45143 86.41299 assigned negative charge : -367.4577 centred at (gu) : 86.75783 92.90339 86.39555 start vw surface at 0.1100000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 152378 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22789 grid for indexing accessible points = 1.400000 m= 71721 mr = 107609 m= 23151 mr = 57001 m= 4712 mr = 17597 m= 553 mr = 3213 m= 26 mr = 283 m= 0 mr = 4 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.400000 number of dielectric boundary points 66834 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 18525 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) : 1.830177 object centre at (A) : 18.76600 3.872499 36.70500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7171389 0.1230829 midg,1,midg; midg,igrid,midg -4.7131304E-02 0.2067760 1,midg,midg; igrid,midg,midg -4.6847276E-02 0.1076616 gauss-seidel spectral radius is 0.9992195 estimated iterations to convergence 283 setup time was (sec) 1.730000 now iterating at: 14:42:42 rms-change max change #iterations 9.130575 400.2593 at 10iterations 5.261934 111.8613 at 20iterations 3.004346 62.14888 at 30iterations 1.715608 41.15269 at 40iterations 0.9733323 18.76000 at 50iterations 0.5543858 11.47902 at 60iterations 0.3135071 7.102814 at 70iterations 0.1782110 3.734328 at 80iterations 0.1008072 1.919861 at 90iterations 5.7036240E-02 1.041093 at 100iterations 3.2241885E-02 0.6627226 at 110iterations 1.8254280E-02 0.3863688 at 120iterations 1.0319135E-02 0.1973801 at 130iterations 5.8339713E-03 0.1225455 at 140iterations 3.2940556E-03 6.2587738E-02 at 150iterations 1.8648223E-03 3.5391808E-02 at 160iterations 1.0535870E-03 2.1636963E-02 at 170iterations 5.9474586E-04 1.2008667E-02 at 180iterations finished qdiffx linear iterations at : 14:42:59 total time elapsed so far: 17.96000 # loops : 180 mean,max change (kT/e) : 5.9474586E-04 1.2008667E-02 energy calculations done at 17.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.13000 DelPhi exited at 14:42:59 18.138u 0.490s 0:18.96 98.2% 0+0k 0+0io 0pf+0w