Tue Oct 11 06:23:36 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 Tue Oct 11 2011 at 06:23:36 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2045 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7175683 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): 3.378000 47.25000 ymin,ymax (A): 0.6230000 42.32800 zmin,zma (A): -2.586000 47.02600 x,y,z range (A): 43.87200 41.70500 49.61200 scale (grids/A): 0.7175683 object centre (A): 25.31400 21.47550 22.22000 number of atom coordinates read : 2045 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 311.3571 centred at (gu) : 89.85786 89.94847 90.29397 assigned negative charge : -304.4261 centred at (gu) : 90.04749 89.92599 90.32108 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7190 nv = 96 ne = 84 npr = 41112 no. pairs analyzed = 41112 no. exposed pairs = 2458 no. arc points = 16743 no. surface atoms = 842 nbur = 1203 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 468 mr = 4196 m= 9 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3393 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1598 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7898 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.5542077E-08 6.0856557E-08 midg,1,midg; midg,igrid,midg 6.1055481E-08 8.6765347E-08 1,midg,midg; igrid,midg,midg 1.9151025E-07 -4.1169333E-08 gauss-seidel spectral radius is 0.9898704 estimated iterations to convergence 81 setup time was (sec) 0.3600000 now iterating at: 06:23:37 rms-change max change #iterations 0.2180723 30.22833 at 10iterations 2.7981510E-02 3.855718 at 20iterations 3.8824719E-03 0.5706253 at 30iterations 6.7270274E-04 8.5174561E-02 at 40iterations 1.6223543E-04 1.9989014E-02 at 50iterations finished qdiffx linear iterations at : 06:23:40 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.6223543E-04 1.9989014E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 06:23:40 3.370u 0.168s 0:03.86 91.4% 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 Tue Oct 11 2011 at 06:23:40 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2045 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.152705 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): 3.378000 47.25000 ymin,ymax (A): 0.6230000 42.32800 zmin,zma (A): -2.586000 47.02600 x,y,z range (A): 43.87200 41.70500 49.61200 scale (grids/A): 2.152705 object centre (A): 25.31400 21.47550 22.22000 number of atom coordinates read : 2045 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 311.3571 centred at (gu) : 89.57372 89.84550 90.88183 assigned negative charge : -304.4261 centred at (gu) : 90.14246 89.77802 90.96336 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 76244 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16743 grid for indexing accessible points = 1.400000 m= 30823 mr = 54572 m= 6192 mr = 23622 m= 554 mr = 4074 m= 13 mr = 259 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 31299 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 68 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 15286 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) : 0.7175683 object centre at (A) : 25.31400 21.47550 22.22000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5376664E-02 6.9653928E-02 midg,1,midg; midg,igrid,midg 5.8225440E-03 2.6405569E-02 1,midg,midg; igrid,midg,midg 4.8497595E-02 5.3167627E-03 gauss-seidel spectral radius is 0.9988553 estimated iterations to convergence 234 setup time was (sec) 0.6000000 now iterating at: 06:23:41 rms-change max change #iterations 4.649330 206.7940 at 10iterations 2.314344 73.78383 at 20iterations 1.162512 36.97346 at 30iterations 0.5779175 18.43571 at 40iterations 0.2911738 8.987629 at 50iterations 0.1453495 4.402573 at 60iterations 7.2930187E-02 2.366573 at 70iterations 3.6439460E-02 1.250000 at 80iterations 1.8336313E-02 0.5155602 at 90iterations 9.2967963E-03 0.2609320 at 100iterations 4.7534397E-03 0.1546174 at 110iterations 2.4620998E-03 7.3059082E-02 at 120iterations finished qdiffx linear iterations at : 06:23:48 total time elapsed so far: 7.700000 # loops : 120 mean,max change (kT/e) : 2.4620998E-03 7.3059082E-02 energy calculations done at 7.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 06:23:48 7.836u 0.210s 0:08.32 96.6% 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 Tue Oct 11 2011 at 06:23:48 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2045 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.229058 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): 3.378000 47.25000 ymin,ymax (A): 0.6230000 42.32800 zmin,zma (A): -2.586000 47.02600 x,y,z range (A): 43.87200 41.70500 49.61200 scale (grids/A): 3.229058 object centre (A): 25.31400 21.47550 22.22000 number of atom coordinates read : 2045 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 311.3571 centred at (gu) : 89.36050 89.76831 91.32281 assigned negative charge : -304.4261 centred at (gu) : 90.21371 89.66705 91.44507 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 175626 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16743 grid for indexing accessible points = 1.400000 m= 96220 mr = 131157 m= 39542 mr = 80504 m= 11700 mr = 32626 m= 2325 mr = 9043 m= 260 mr = 1584 m= 6 mr = 170 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.180000 number of dielectric boundary points 70595 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 15384 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) : 2.152705 object centre at (A) : 25.31400 21.47550 22.22000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4673465 0.6295999 midg,1,midg; midg,igrid,midg -1.0764733E-02 0.2022623 1,midg,midg; igrid,midg,midg 0.3375666 0.1553711 gauss-seidel spectral radius is 0.9992982 estimated iterations to convergence 298 setup time was (sec) 1.420000 now iterating at: 06:23:50 rms-change max change #iterations 10.29625 314.0945 at 10iterations 6.111495 135.8032 at 20iterations 3.616391 73.19529 at 30iterations 2.131395 39.68918 at 40iterations 1.255022 24.05424 at 50iterations 0.7396939 13.77850 at 60iterations 0.4353693 7.458504 at 70iterations 0.2555869 4.466112 at 80iterations 0.1500615 3.122181 at 90iterations 8.8308960E-02 1.705221 at 100iterations 5.2105173E-02 0.9069881 at 110iterations 3.0863428E-02 0.5210438 at 120iterations 1.8539833E-02 0.3583279 at 130iterations 1.1358872E-02 0.2005348 at 140iterations 7.2081843E-03 0.1312542 at 150iterations 4.7920207E-03 0.1003342 at 160iterations 3.3823189E-03 6.6154480E-02 at 170iterations 2.5276004E-03 4.7866821E-02 at 180iterations finished qdiffx linear iterations at : 06:24:01 total time elapsed so far: 12.70000 # loops : 180 mean,max change (kT/e) : 2.5276004E-03 4.7866821E-02 energy calculations done at 12.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.84000 DelPhi exited at 06:24:02 12.844u 0.202s 0:13.33 97.8% 0+0k 0+0io 0pf+0w