Mon Oct 10 23:15:29 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 23:15:29 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2631 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: ASP 298 has a net charge of -2.0000 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: 0.6114107 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): 0.9690000 55.60200 ymin,ymax (A): -16.66200 41.56400 zmin,zma (A): 56.52600 98.28700 x,y,z range (A): 54.63300 58.22601 41.76100 scale (grids/A): 0.6114107 object centre (A): 28.28550 12.45100 77.40650 number of atom coordinates read : 2631 total number of charged atoms : 2511 net assigned charge : 4.406015 assigned positive charge : 400.4608 centred at (gu) : 90.36442 90.00862 89.74480 assigned negative charge : -396.0553 centred at (gu) : 90.16147 89.95629 89.57111 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6651 nv = 96 ne = 84 npr = 51956 no. pairs analyzed = 51956 no. exposed pairs = 3233 no. arc points = 22831 no. surface atoms = 1086 nbur = 1545 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 291 mr = 3675 m= 3 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.3100000 number of dielectric boundary points 3247 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2324 ## 260 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8171 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.0213018E-09 1.1050344E-08 midg,1,midg; midg,igrid,midg -5.1202324E-11 5.4761569E-09 1,midg,midg; igrid,midg,midg -7.5609732E-09 1.4306394E-08 gauss-seidel spectral radius is 0.9861547 estimated iterations to convergence 70 setup time was (sec) 0.6300000 now iterating at: 23:15:30 rms-change max change #iterations 0.1241880 18.19889 at 10iterations 1.1613723E-02 1.754818 at 20iterations 1.4456416E-03 0.2901039 at 30iterations 3.5105564E-04 8.0646515E-02 at 40iterations 9.8333294E-05 2.3864746E-02 at 50iterations finished qdiffx linear iterations at : 23:15:34 total time elapsed so far: 4.300000 # loops : 50 mean,max change (kT/e) : 9.8333294E-05 2.3864746E-02 energy calculations done at 4.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.470000 DelPhi exited at 23:15:34 4.474u 0.389s 0:05.30 91.5% 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 23:15:34 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2631 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: ASP 298 has a net charge of -2.0000 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: 1.834232 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): 0.9690000 55.60200 ymin,ymax (A): -16.66200 41.56400 zmin,zma (A): 56.52600 98.28700 x,y,z range (A): 54.63300 58.22601 41.76100 scale (grids/A): 1.834232 object centre (A): 28.28550 12.45100 77.40650 number of atom coordinates read : 2631 total number of charged atoms : 2511 net assigned charge : 4.406015 assigned positive charge : 400.4608 centred at (gu) : 91.09285 90.02506 89.23380 assigned negative charge : -396.0553 centred at (gu) : 90.48413 89.86854 88.71290 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 72175 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22831 grid for indexing accessible points = 1.400000 m= 25661 mr = 50191 m= 3630 mr = 19087 m= 130 mr = 2236 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 2199 time to turn everything in is 0.5800000 number of dielectric boundary points 30055 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 156 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 19605 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) : 0.6114107 object centre at (A) : 28.28550 12.45100 77.40650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3063386E-03 2.4758495E-02 midg,1,midg; midg,igrid,midg -1.8552013E-02 1.8027715E-02 1,midg,midg; igrid,midg,midg -2.0755809E-02 5.5750798E-02 gauss-seidel spectral radius is 0.9985378 estimated iterations to convergence 207 setup time was (sec) 0.8700000 now iterating at: 23:15:36 rms-change max change #iterations 4.037345 155.7281 at 10iterations 1.831678 61.57613 at 20iterations 0.8346279 27.73935 at 30iterations 0.3799896 12.01491 at 40iterations 0.1731112 5.895180 at 50iterations 7.9227760E-02 2.577694 at 60iterations 3.6470294E-02 1.321388 at 70iterations 1.6683813E-02 0.6119308 at 80iterations 7.7535980E-03 0.2914886 at 90iterations 3.6754343E-03 0.1281509 at 100iterations 1.8219702E-03 7.4047089E-02 at 110iterations 9.6966600E-04 4.2238235E-02 at 120iterations finished qdiffx linear iterations at : 23:15:45 total time elapsed so far: 10.15000 # loops : 120 mean,max change (kT/e) : 9.6966600E-04 4.2238235E-02 energy calculations done at 10.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.31000 DelPhi exited at 23:15:45 10.311u 0.465s 0:11.22 95.9% 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 23:15:46 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2631 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: ASP 298 has a net charge of -2.0000 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: 2.751348 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): 0.9690000 55.60200 ymin,ymax (A): -16.66200 41.56400 zmin,zma (A): 56.52600 98.28700 x,y,z range (A): 54.63300 58.22601 41.76100 scale (grids/A): 2.751348 object centre (A): 28.28550 12.45100 77.40650 number of atom coordinates read : 2631 total number of charged atoms : 2511 net assigned charge : 4.406015 assigned positive charge : 400.4608 centred at (gu) : 91.63924 90.03758 88.85078 assigned negative charge : -396.0553 centred at (gu) : 90.72610 89.80273 88.06932 start vw surface at 0.1200000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 167092 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22831 grid for indexing accessible points = 1.400000 m= 84416 mr = 121819 m= 29326 mr = 69617 m= 6445 mr = 23572 m= 655 mr = 4819 m= 15 mr = 361 m= 0 mr = 4 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 7785 time to turn everything in is 1.490000 number of dielectric boundary points 67757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 20088 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) : 1.834232 object centre at (A) : 28.28550 12.45100 77.40650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.0995232E-02 0.2579602 midg,1,midg; midg,igrid,midg -0.2106806 0.3209335 1,midg,midg; igrid,midg,midg -0.1921244 0.8462249 gauss-seidel spectral radius is 0.9992313 estimated iterations to convergence 285 setup time was (sec) 1.800000 now iterating at: 23:15:48 rms-change max change #iterations 9.571062 329.8813 at 10iterations 5.498764 132.8474 at 20iterations 3.149333 68.89858 at 30iterations 1.798164 38.90769 at 40iterations 1.024336 19.85248 at 50iterations 0.5838915 11.50811 at 60iterations 0.3327107 6.381842 at 70iterations 0.1893982 3.403070 at 80iterations 0.1077596 2.284214 at 90iterations 6.1207004E-02 1.224862 at 100iterations 3.4834523E-02 0.6367359 at 110iterations 1.9823397E-02 0.3841362 at 120iterations 1.1289143E-02 0.2271175 at 130iterations 6.4704977E-03 0.1301270 at 140iterations 3.7055602E-03 7.9624176E-02 at 150iterations 2.1550485E-03 4.5028687E-02 at 160iterations 1.2791881E-03 2.8495789E-02 at 170iterations 7.8749127E-04 1.8554688E-02 at 180iterations finished qdiffx linear iterations at : 23:16:03 total time elapsed so far: 17.21000 # loops : 180 mean,max change (kT/e) : 7.8749127E-04 1.8554688E-02 energy calculations done at 17.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.37000 DelPhi exited at 23:16:04 17.378u 0.484s 0:18.15 98.3% 0+0k 0+0io 0pf+0w