Sun Oct 9 08:16:08 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 Sun Oct 9 2011 at 08:16:09 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5285 !!! WARNING: HIR 704 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5161066 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): -16.87300 46.59600 ymin,ymax (A): 4.162000 73.14000 zmin,zma (A): -110.4990 -46.39200 x,y,z range (A): 63.46899 68.97800 64.10699 scale (grids/A): 0.5161066 object centre (A): 14.86150 38.65100 -78.44550 number of atom coordinates read : 5285 total number of charged atoms : 5120 net assigned charge : -5.485989 assigned positive charge : 796.0605 centred at (gu) : 90.74567 90.05118 89.18161 assigned negative charge : -801.5528 centred at (gu) : 90.71753 90.05307 89.08202 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8892 nv = 96 ne = 84 npr = 106262 no. pairs analyzed = 106262 no. exposed pairs = 6884 no. arc points = 47710 no. surface atoms = 2289 nbur = 2996 mkacc time = 0.2300000 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 = 1.652000 m= 349 mr = 4496 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.4900000 number of dielectric boundary points 4735 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4674 ## 680 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 12022 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7988886E-10 2.1226554E-10 midg,1,midg; midg,igrid,midg -8.8512128E-11 -1.0491610E-10 1,midg,midg; igrid,midg,midg -1.6524190E-10 8.7791692E-12 gauss-seidel spectral radius is 0.9808389 estimated iterations to convergence 60 setup time was (sec) 0.7200000 now iterating at: 08:16:09 rms-change max change #iterations 7.7535614E-02 10.06317 at 10iterations 4.8005944E-03 0.7151718 at 20iterations 6.5706921E-04 0.1498241 at 30iterations 1.9776251E-04 4.7964096E-02 at 40iterations 6.5547065E-05 1.5792847E-02 at 50iterations finished qdiffx linear iterations at : 08:16:12 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 6.5547065E-05 1.5792847E-02 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 08:16:13 3.524u 0.172s 0:04.12 89.5% 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 Sun Oct 9 2011 at 08:16:13 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5285 !!! WARNING: HIR 704 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.548320 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): -16.87300 46.59600 ymin,ymax (A): 4.162000 73.14000 zmin,zma (A): -110.4990 -46.39200 x,y,z range (A): 63.46899 68.97800 64.10699 scale (grids/A): 1.548320 object centre (A): 14.86150 38.65100 -78.44550 number of atom coordinates read : 5285 total number of charged atoms : 5120 net assigned charge : -5.485989 assigned positive charge : 796.0605 centred at (gu) : 92.23586 90.15179 87.54341 assigned negative charge : -801.5528 centred at (gu) : 92.15250 90.15873 87.24584 start vw surface at 0.2300000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 99853 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47710 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 29381 mr = 67380 m= 2767 mr = 19379 m= 45 mr = 1165 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 860 time to turn everything in is 0.7300000 number of dielectric boundary points 44122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 631 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 38612 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) : 0.5161066 object centre at (A) : 14.86150 38.65100 -78.44550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8570322E-02 9.1035096E-03 midg,1,midg; midg,igrid,midg -5.8543403E-03 -1.8867346E-02 1,midg,midg; igrid,midg,midg -2.0150482E-03 -8.3846385E-03 gauss-seidel spectral radius is 0.9982127 estimated iterations to convergence 188 setup time was (sec) 1.040000 now iterating at: 08:16:14 rms-change max change #iterations 4.130004 155.9846 at 10iterations 1.735543 55.16956 at 20iterations 0.7266538 23.23753 at 30iterations 0.3045712 9.268158 at 40iterations 0.1276033 3.996773 at 50iterations 5.3863492E-02 1.621252 at 60iterations 2.2640342E-02 0.7053628 at 70iterations 9.5479526E-03 0.3139615 at 80iterations 4.0592370E-03 0.1214046 at 90iterations 1.7336363E-03 5.6707382E-02 at 100iterations 7.6096499E-04 2.6916504E-02 at 110iterations 3.4764953E-04 1.3343811E-02 at 120iterations finished qdiffx linear iterations at : 08:16:21 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 3.4764953E-04 1.3343811E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 08:16:21 7.999u 0.226s 0:08.53 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 Sun Oct 9 2011 at 08:16:21 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5285 !!! WARNING: HIR 704 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.322480 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): -16.87300 46.59600 ymin,ymax (A): 4.162000 73.14000 zmin,zma (A): -110.4990 -46.39200 x,y,z range (A): 63.46899 68.97800 64.10699 scale (grids/A): 2.322480 object centre (A): 14.86150 38.65100 -78.44550 number of atom coordinates read : 5285 total number of charged atoms : 5120 net assigned charge : -5.485989 assigned positive charge : 796.0605 centred at (gu) : 93.35326 90.22713 86.31466 assigned negative charge : -801.5528 centred at (gu) : 93.22878 90.23806 85.86868 start vw surface at 0.2000000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 232160 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47710 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 103467 mr = 165411 m= 27296 mr = 79833 m= 3952 mr = 19778 m= 208 mr = 2447 m= 3 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 2821 time to turn everything in is 1.730000 number of dielectric boundary points 99549 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 74 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 40834 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) : 1.548320 object centre at (A) : 14.86150 38.65100 -78.44550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5433801 0.1128475 midg,1,midg; midg,igrid,midg -1.1170679E-02 -0.6197416 1,midg,midg; igrid,midg,midg -0.1188845 -0.1184581 gauss-seidel spectral radius is 0.9992098 estimated iterations to convergence 281 setup time was (sec) 2.060000 now iterating at: 08:16:24 rms-change max change #iterations 11.17266 318.4319 at 10iterations 6.554701 138.7635 at 20iterations 3.810926 76.44898 at 30iterations 2.195055 40.40842 at 40iterations 1.261866 22.74994 at 50iterations 0.7234773 14.76761 at 60iterations 0.4131310 7.496433 at 70iterations 0.2351042 4.681801 at 80iterations 0.1339158 2.535113 at 90iterations 7.6124437E-02 1.355270 at 100iterations 4.3154277E-02 0.7449260 at 110iterations 2.4537235E-02 0.4638901 at 120iterations 1.3885372E-02 0.2430496 at 130iterations 7.8610005E-03 0.1415844 at 140iterations 4.4668070E-03 7.6950073E-02 at 150iterations 2.5240218E-03 4.1894913E-02 at 160iterations 1.4316171E-03 2.5741577E-02 at 170iterations 8.1172917E-04 1.3233185E-02 at 180iterations finished qdiffx linear iterations at : 08:16:35 total time elapsed so far: 13.42000 # loops : 180 mean,max change (kT/e) : 8.1172917E-04 1.3233185E-02 energy calculations done at 13.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.59000 DelPhi exited at 08:16:36 13.594u 0.296s 0:14.19 97.8% 0+0k 0+0io 0pf+0w