Sat Oct 8 22:51:23 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 Sat Oct 8 2011 at 22:51:23 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3254 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5735645 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): -16.25900 40.46400 ymin,ymax (A): 16.96700 76.48100 zmin,zma (A): 25.45500 87.52300 x,y,z range (A): 56.72300 59.51400 62.06800 scale (grids/A): 0.5735645 object centre (A): 12.10250 46.72400 56.48900 number of atom coordinates read : 3254 total number of charged atoms : 3112 net assigned charge : 11.97103 assigned positive charge : 481.4148 centred at (gu) : 89.89111 90.14501 90.59721 assigned negative charge : -469.4453 centred at (gu) : 89.74513 90.21320 90.77490 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7336 nv = 96 ne = 84 npr = 63596 no. pairs analyzed = 63596 no. exposed pairs = 4317 no. arc points = 31251 no. surface atoms = 1438 nbur = 1816 mkacc time = 0.1400000 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 = 1.484000 m= 321 mr = 3702 m= 3 mr = 26 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 0.3400000 number of dielectric boundary points 3932 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3202 ## 371 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9292 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6743014E-09 -1.4987479E-09 midg,1,midg; midg,igrid,midg 3.2746126E-09 8.5772323E-10 1,midg,midg; igrid,midg,midg -6.8447092E-10 4.6862207E-09 gauss-seidel spectral radius is 0.9843506 estimated iterations to convergence 66 setup time was (sec) 0.5400000 now iterating at: 22:51:24 rms-change max change #iterations 9.9871710E-02 17.70964 at 10iterations 7.5293062E-03 1.158699 at 20iterations 5.8452185E-04 8.9353323E-02 at 30iterations 5.2220224E-05 7.7743530E-03 at 40iterations 6.2863805E-06 6.8283081E-04 at 50iterations finished qdiffx linear iterations at : 22:51:26 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 6.2863805E-06 6.8283081E-04 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 22:51:27 3.103u 0.167s 0:03.59 90.8% 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 Sat Oct 8 2011 at 22:51:27 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3254 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.720693 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): -16.25900 40.46400 ymin,ymax (A): 16.96700 76.48100 zmin,zma (A): 25.45500 87.52300 x,y,z range (A): 56.72300 59.51400 62.06800 scale (grids/A): 1.720693 object centre (A): 12.10250 46.72400 56.48900 number of atom coordinates read : 3254 total number of charged atoms : 3112 net assigned charge : 11.97103 assigned positive charge : 481.4148 centred at (gu) : 89.67267 90.43427 91.79072 assigned negative charge : -469.4453 centred at (gu) : 89.23524 90.63933 92.32449 start vw surface at 0.1900000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 80654 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31251 grid for indexing accessible points = 1.400000 m= 25859 mr = 53930 m= 3126 mr = 17820 m= 109 mr = 1610 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 569 time to turn everything in is 0.5700000 number of dielectric boundary points 36383 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 295 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 24090 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) : 0.5735645 object centre at (A) : 12.10250 46.72400 56.48900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7979143E-02 7.2108493E-03 midg,1,midg; midg,igrid,midg 3.6631986E-02 7.3088063E-03 1,midg,midg; igrid,midg,midg -8.1866654E-03 1.5285491E-02 gauss-seidel spectral radius is 0.9984173 estimated iterations to convergence 199 setup time was (sec) 0.8300000 now iterating at: 22:51:28 rms-change max change #iterations 3.901170 178.4651 at 10iterations 1.710480 55.43679 at 20iterations 0.7555299 23.86354 at 30iterations 0.3315630 11.03380 at 40iterations 0.1461888 4.625074 at 50iterations 6.4394802E-02 2.058805 at 60iterations 2.8453939E-02 0.9447212 at 70iterations 1.2576209E-02 0.4316444 at 80iterations 5.5298004E-03 0.1866398 at 90iterations 2.4477735E-03 7.9833508E-02 at 100iterations 1.0792111E-03 3.6067963E-02 at 110iterations 4.7782820E-04 1.4575958E-02 at 120iterations finished qdiffx linear iterations at : 22:51:34 total time elapsed so far: 7.050000 # loops : 120 mean,max change (kT/e) : 4.7782820E-04 1.4575958E-02 energy calculations done at 7.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.220000 DelPhi exited at 22:51:34 7.226u 0.146s 0:07.65 96.2% 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 22:51:34 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3254 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 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: 2.581040 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): -16.25900 40.46400 ymin,ymax (A): 16.96700 76.48100 zmin,zma (A): 25.45500 87.52300 x,y,z range (A): 56.72300 59.51400 62.06800 scale (grids/A): 2.581040 object centre (A): 12.10250 46.72400 56.48900 number of atom coordinates read : 3254 total number of charged atoms : 3112 net assigned charge : 11.97103 assigned positive charge : 481.4148 centred at (gu) : 89.50904 90.65129 92.68583 assigned negative charge : -469.4453 centred at (gu) : 88.85287 90.95896 93.48668 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 186986 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31251 grid for indexing accessible points = 1.400000 m= 87920 mr = 132064 m= 27031 mr = 69315 m= 5019 mr = 20410 m= 482 mr = 3351 m= 12 mr = 254 m= 0 mr = 4 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 2005 time to turn everything in is 1.300000 number of dielectric boundary points 82052 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 24868 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) : 1.720693 object centre at (A) : 12.10250 46.72400 56.48900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7463551 7.7360027E-02 midg,1,midg; midg,igrid,midg 0.6109729 0.2426690 1,midg,midg; igrid,midg,midg -6.6031925E-02 0.2189064 gauss-seidel spectral radius is 0.9992233 estimated iterations to convergence 283 setup time was (sec) 1.590000 now iterating at: 22:51:36 rms-change max change #iterations 9.752208 315.8951 at 10iterations 5.665835 138.8952 at 20iterations 3.266157 75.04996 at 30iterations 1.874833 40.98067 at 40iterations 1.072707 24.17835 at 50iterations 0.6121038 12.65340 at 60iterations 0.3475249 6.598577 at 70iterations 0.1979138 4.095497 at 80iterations 0.1125503 2.308584 at 90iterations 6.3847922E-02 1.252023 at 100iterations 3.6289372E-02 0.6369982 at 110iterations 2.0548934E-02 0.4085445 at 120iterations 1.1653198E-02 0.2131329 at 130iterations 6.6032475E-03 0.1449280 at 140iterations 3.7445528E-03 6.7262650E-02 at 150iterations 2.1138319E-03 3.9299548E-02 at 160iterations 1.2010405E-03 2.2537231E-02 at 170iterations 6.8057684E-04 1.2081146E-02 at 180iterations finished qdiffx linear iterations at : 22:51:46 total time elapsed so far: 11.11000 # loops : 180 mean,max change (kT/e) : 6.8057684E-04 1.2081146E-02 energy calculations done at 11.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.28000 DelPhi exited at 22:51:46 11.286u 0.163s 0:11.79 97.0% 0+0k 0+0io 0pf+0w