Mon Oct 10 19:31:57 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 19:31:57 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2424 !!! WARNING: GLM 776 has a net charge of -0.0940 !!! WARNING: SEP 810 has a net charge of -0.4750 !!! WARNING: GLU 1441 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6444606 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): -0.3920001 50.65300 ymin,ymax (A): 51.17800 96.03400 zmin,zma (A): -17.68500 37.55500 x,y,z range (A): 51.04500 44.85600 55.24000 scale (grids/A): 0.6444606 object centre (A): 25.13050 73.60600 9.935000 number of atom coordinates read : 2424 total number of charged atoms : 2342 net assigned charge : -3.568997 assigned positive charge : 360.0759 centred at (gu) : 87.92785 89.57441 88.70255 assigned negative charge : -363.6458 centred at (gu) : 87.97620 89.58258 88.77654 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6781 nv = 96 ne = 84 npr = 48814 no. pairs analyzed = 48814 no. exposed pairs = 3097 no. arc points = 21358 no. surface atoms = 1044 nbur = 1380 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 429 mr = 3734 m= 1 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.2800000 number of dielectric boundary points 3406 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2135 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8231 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9183941E-09 -1.1618719E-08 midg,1,midg; midg,igrid,midg -5.5977600E-09 -6.5342833E-09 1,midg,midg; igrid,midg,midg -1.4746611E-10 -7.8474365E-09 gauss-seidel spectral radius is 0.9875119 estimated iterations to convergence 73 setup time was (sec) 0.5100000 now iterating at: 19:31:58 rms-change max change #iterations 0.1448803 21.77378 at 10iterations 1.4587828E-02 2.051744 at 20iterations 1.5121731E-03 0.2197609 at 30iterations 1.6549924E-04 2.2979736E-02 at 40iterations 2.4007833E-05 3.1490326E-03 at 50iterations finished qdiffx linear iterations at : 19:32:00 total time elapsed so far: 3.010000 # loops : 50 mean,max change (kT/e) : 2.4007833E-05 3.1490326E-03 energy calculations done at 3.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.180000 DelPhi exited at 19:32:01 3.186u 0.176s 0:03.92 85.4% 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 Mon Oct 10 2011 at 19:32:01 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2424 !!! WARNING: GLM 776 has a net charge of -0.0940 !!! WARNING: SEP 810 has a net charge of -0.4750 !!! WARNING: GLU 1441 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: 1.933382 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): -0.3920001 50.65300 ymin,ymax (A): 51.17800 96.03400 zmin,zma (A): -17.68500 37.55500 x,y,z range (A): 51.04500 44.85600 55.24000 scale (grids/A): 1.933382 object centre (A): 25.13050 73.60600 9.935000 number of atom coordinates read : 2424 total number of charged atoms : 2342 net assigned charge : -3.568997 assigned positive charge : 360.0759 centred at (gu) : 83.78291 88.72260 86.10713 assigned negative charge : -363.6458 centred at (gu) : 83.92849 88.74756 86.32964 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 73527 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21358 grid for indexing accessible points = 1.400000 m= 27426 mr = 50974 m= 4800 mr = 20325 m= 334 mr = 3157 m= 3 mr = 155 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.5200000 number of dielectric boundary points 31479 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 18468 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) : 0.6444606 object centre at (A) : 25.13050 73.60600 9.935000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6634909E-02 -1.6574325E-02 midg,1,midg; midg,igrid,midg -1.2658775E-02 -2.0819850E-02 1,midg,midg; igrid,midg,midg 1.3958954E-02 -3.5696230E-03 gauss-seidel spectral radius is 0.9986599 estimated iterations to convergence 216 setup time was (sec) 0.8000000 now iterating at: 19:32:02 rms-change max change #iterations 4.196118 161.3060 at 10iterations 1.977736 67.97666 at 20iterations 0.9323378 32.74357 at 30iterations 0.4402283 14.89363 at 40iterations 0.2080156 6.841464 at 50iterations 9.8382257E-02 3.136639 at 60iterations 4.6477322E-02 1.589371 at 70iterations 2.1942444E-02 0.6520290 at 80iterations 1.0372395E-02 0.3380182 at 90iterations 4.8807710E-03 0.1685047 at 100iterations 2.3159862E-03 6.9575787E-02 at 110iterations 1.0896688E-03 3.2374144E-02 at 120iterations finished qdiffx linear iterations at : 19:32:08 total time elapsed so far: 6.920000 # loops : 120 mean,max change (kT/e) : 1.0896688E-03 3.2374144E-02 energy calculations done at 6.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.100000 DelPhi exited at 19:32:09 7.107u 0.226s 0:08.36 87.5% 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 19:32:09 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2424 !!! WARNING: GLM 776 has a net charge of -0.0940 !!! WARNING: SEP 810 has a net charge of -0.4750 !!! WARNING: GLU 1441 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.900073 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): -0.3920001 50.65300 ymin,ymax (A): 51.17800 96.03400 zmin,zma (A): -17.68500 37.55500 x,y,z range (A): 51.04500 44.85600 55.24000 scale (grids/A): 2.900073 object centre (A): 25.13050 73.60600 9.935000 number of atom coordinates read : 2424 total number of charged atoms : 2342 net assigned charge : -3.568997 assigned positive charge : 360.0759 centred at (gu) : 80.67425 88.08384 84.16068 assigned negative charge : -363.6458 centred at (gu) : 80.89259 88.12148 84.49437 start vw surface at 0.1200000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 169929 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21358 grid for indexing accessible points = 1.400000 m= 86692 mr = 123608 m= 33473 mr = 70842 m= 8783 mr = 27200 m= 1477 mr = 6796 m= 127 mr = 1047 m= 3 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 68 time to turn everything in is 1.320000 number of dielectric boundary points 70928 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 18732 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) : 1.933382 object centre at (A) : 25.13050 73.60600 9.935000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2200854 -4.7200087E-02 midg,1,midg; midg,igrid,midg -4.8619516E-02 -0.2349955 1,midg,midg; igrid,midg,midg 4.2230885E-02 3.1168421E-03 gauss-seidel spectral radius is 0.9992693 estimated iterations to convergence 292 setup time was (sec) 1.650000 now iterating at: 19:32:11 rms-change max change #iterations 9.813809 426.1127 at 10iterations 5.730160 121.2365 at 20iterations 3.338845 63.12645 at 30iterations 1.948256 37.54979 at 40iterations 1.132533 20.43933 at 50iterations 0.6575552 12.35684 at 60iterations 0.3805887 7.125929 at 70iterations 0.2208546 4.287140 at 80iterations 0.1277055 2.242947 at 90iterations 7.3789068E-02 1.374450 at 100iterations 4.2632505E-02 0.7578036 at 110iterations 2.4621882E-02 0.4744158 at 120iterations 1.4194860E-02 0.2671547 at 130iterations 8.2136886E-03 0.1396255 at 140iterations 4.7473982E-03 8.1449330E-02 at 150iterations 2.7435638E-03 5.3588867E-02 at 160iterations 1.5874380E-03 2.7260303E-02 at 170iterations 9.2062389E-04 1.7496109E-02 at 180iterations finished qdiffx linear iterations at : 19:32:22 total time elapsed so far: 12.31000 # loops : 180 mean,max change (kT/e) : 9.2062389E-04 1.7496109E-02 energy calculations done at 12.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.55000 DelPhi exited at 19:32:23 12.553u 0.246s 0:13.41 95.3% 0+0k 0+0io 0pf+0w