Sat Oct 8 11:35:56 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 Sat Oct 8 2011 at 11:35:56 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 = 4364 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5666083 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): 60.06000 115.6130 ymin,ymax (A): 20.75100 83.14200 zmin,zma (A): -7.689000 55.14100 x,y,z range (A): 55.55300 62.39100 62.83000 scale (grids/A): 0.5666083 object centre (A): 87.83650 51.94650 23.72600 number of atom coordinates read : 4364 total number of charged atoms : 4216 net assigned charge : -1.999943 assigned positive charge : 656.0702 centred at (gu) : 89.51431 90.10980 89.80935 assigned negative charge : -658.0734 centred at (gu) : 89.71893 90.06585 89.64331 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8894 nv = 96 ne = 84 npr = 91634 no. pairs analyzed = 91634 no. exposed pairs = 4924 no. arc points = 33403 no. surface atoms = 1655 nbur = 2709 mkacc time = 0.1600000 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 = 1.512000 m= 385 mr = 5164 m= 2 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 119 time to turn everything in is 0.3000000 number of dielectric boundary points 4080 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3507 ## 446 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 11888 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9686352E-09 2.9484193E-09 midg,1,midg; midg,igrid,midg -1.1641758E-09 6.4203087E-10 1,midg,midg; igrid,midg,midg 4.3386765E-09 -4.1107060E-09 gauss-seidel spectral radius is 0.9840280 estimated iterations to convergence 65 setup time was (sec) 0.5100000 now iterating at: 11:35:56 rms-change max change #iterations 0.1086368 18.96317 at 10iterations 8.5411957E-03 1.322271 at 20iterations 1.0650533E-03 0.1401825 at 30iterations 2.9205225E-04 3.7107468E-02 at 40iterations 1.0188857E-04 1.3966560E-02 at 50iterations finished qdiffx linear iterations at : 11:35:59 total time elapsed so far: 3.530000 # loops : 50 mean,max change (kT/e) : 1.0188857E-04 1.3966560E-02 energy calculations done at 3.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.670000 DelPhi exited at 11:36:00 3.673u 0.188s 0:04.42 87.1% 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 Sat Oct 8 2011 at 11:36:00 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 = 4364 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.699825 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): 60.06000 115.6130 ymin,ymax (A): 20.75100 83.14200 zmin,zma (A): -7.689000 55.14100 x,y,z range (A): 55.55300 62.39100 62.83000 scale (grids/A): 1.699825 object centre (A): 87.83650 51.94650 23.72600 number of atom coordinates read : 4364 total number of charged atoms : 4216 net assigned charge : -1.999943 assigned positive charge : 656.0702 centred at (gu) : 88.54174 90.32796 89.42673 assigned negative charge : -658.0734 centred at (gu) : 89.15656 90.19703 88.92953 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 100125 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33403 grid for indexing accessible points = 1.400000 m= 34161 mr = 72627 m= 4260 mr = 25281 m= 127 mr = 2486 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 6463 time to turn everything in is 0.4800000 number of dielectric boundary points 38263 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 337 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 32548 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) : 0.5666083 object centre at (A) : 87.83650 51.94650 23.72600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8427627E-02 2.5337700E-02 midg,1,midg; midg,igrid,midg -3.2277964E-02 3.4657259E-02 1,midg,midg; igrid,midg,midg 3.9023615E-02 -3.5744909E-02 gauss-seidel spectral radius is 0.9984577 estimated iterations to convergence 202 setup time was (sec) 0.7100000 now iterating at: 11:36:01 rms-change max change #iterations 4.497339 158.1245 at 10iterations 2.010988 63.04939 at 20iterations 0.9009755 26.52065 at 30iterations 0.4024269 13.04251 at 40iterations 0.1802304 5.826500 at 50iterations 8.0580637E-02 2.375783 at 60iterations 3.6193881E-02 0.9989185 at 70iterations 1.6243856E-02 0.4812246 at 80iterations 7.3004244E-03 0.2150078 at 90iterations 3.3124003E-03 9.1253281E-02 at 100iterations 1.5272286E-03 4.2179108E-02 at 110iterations 7.2168029E-04 1.9826889E-02 at 120iterations finished qdiffx linear iterations at : 11:36:09 total time elapsed so far: 8.330000 # loops : 120 mean,max change (kT/e) : 7.2168029E-04 1.9826889E-02 energy calculations done at 8.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.460000 DelPhi exited at 11:36:09 8.467u 0.235s 0:09.20 94.4% 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 Sat Oct 8 2011 at 11:36:09 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 = 4364 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.549737 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): 60.06000 115.6130 ymin,ymax (A): 20.75100 83.14200 zmin,zma (A): -7.689000 55.14100 x,y,z range (A): 55.55300 62.39100 62.83000 scale (grids/A): 2.549737 object centre (A): 87.83650 51.94650 23.72600 number of atom coordinates read : 4364 total number of charged atoms : 4216 net assigned charge : -1.999943 assigned positive charge : 656.0702 centred at (gu) : 87.81232 90.49168 89.13959 assigned negative charge : -658.0734 centred at (gu) : 88.73465 90.29536 88.39411 start vw surface at 0.1200000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 232434 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33403 grid for indexing accessible points = 1.400000 m= 115486 mr = 175890 m= 36617 mr = 95269 m= 7112 mr = 29233 m= 556 mr = 5267 m= 11 mr = 247 m= 0 mr = 3 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 22106 time to turn everything in is 1.220000 number of dielectric boundary points 86307 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 33699 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) : 1.699825 object centre at (A) : 87.83650 51.94650 23.72600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3747441 0.2599568 midg,1,midg; midg,igrid,midg -0.8545404 0.7127327 1,midg,midg; igrid,midg,midg 0.6579434 -0.4365631 gauss-seidel spectral radius is 0.9992406 estimated iterations to convergence 286 setup time was (sec) 1.500000 now iterating at: 11:36:11 rms-change max change #iterations 11.26671 291.6563 at 10iterations 6.558130 154.9359 at 20iterations 3.799829 73.19649 at 30iterations 2.201660 40.85448 at 40iterations 1.269109 22.48973 at 50iterations 0.7276988 12.59125 at 60iterations 0.4187450 6.914840 at 70iterations 0.2401167 4.352814 at 80iterations 0.1371784 2.513039 at 90iterations 7.8701496E-02 1.270512 at 100iterations 4.5081627E-02 0.7235565 at 110iterations 2.5835261E-02 0.4157772 at 120iterations 1.4763986E-02 0.2620120 at 130iterations 8.4503591E-03 0.1444111 at 140iterations 4.8598405E-03 7.9917908E-02 at 150iterations 2.8085080E-03 4.9907684E-02 at 160iterations 1.6345293E-03 2.7725220E-02 at 170iterations 9.6425047E-04 1.6014099E-02 at 180iterations finished qdiffx linear iterations at : 11:36:24 total time elapsed so far: 14.29000 # loops : 180 mean,max change (kT/e) : 9.6425047E-04 1.6014099E-02 energy calculations done at 14.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.42000 DelPhi exited at 11:36:26 14.421u 0.322s 0:16.25 90.7% 0+0k 0+0io 0pf+0w