Sat Oct 8 15:55:27 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+sph.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 = amb.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 15:55:27 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2362 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: 0.5842962 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): -2.244000 44.85100 ymin,ymax (A): -15.36800 29.93800 zmin,zma (A): -19.24200 41.68600 x,y,z range (A): 47.09500 45.30600 60.92800 scale (grids/A): 0.5842962 object centre (A): 21.30350 7.285000 11.22200 number of atom coordinates read : 2362 total number of charged atoms : 2285 net assigned charge : 4.000001 assigned positive charge : 351.5241 centred at (gu) : 90.62938 88.72549 88.95647 assigned negative charge : -347.5247 centred at (gu) : 90.66819 88.84982 88.98026 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5246 nv = 96 ne = 84 npr = 48093 no. pairs analyzed = 48093 no. exposed pairs = 2972 no. arc points = 20530 no. surface atoms = 1010 nbur = 1352 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 = 1.456000 m= 231 mr = 2810 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.3100000 number of dielectric boundary points 2649 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2106 ## 229 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 6825 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8383949E-09 4.0525400E-10 midg,1,midg; midg,igrid,midg 4.5868989E-09 -1.1130897E-09 1,midg,midg; igrid,midg,midg 1.5071320E-09 2.3082239E-10 gauss-seidel spectral radius is 0.9848263 estimated iterations to convergence 67 setup time was (sec) 0.6000000 now iterating at: 15:55:28 rms-change max change #iterations 8.7503023E-02 13.75455 at 10iterations 6.9745919E-03 1.309280 at 20iterations 6.1782898E-04 0.1009197 at 30iterations 8.2434482E-05 1.5299082E-02 at 40iterations 1.8300621E-05 3.8380027E-03 at 50iterations finished qdiffx linear iterations at : 15:55:32 total time elapsed so far: 4.010000 # loops : 50 mean,max change (kT/e) : 1.8300621E-05 3.8380027E-03 energy calculations done at 4.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.190000 DelPhi exited at 15:55:32 4.193u 0.296s 0:04.78 93.7% 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 15:55:32 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2362 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: 1.752889 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): -2.244000 44.85100 ymin,ymax (A): -15.36800 29.93800 zmin,zma (A): -19.24200 41.68600 x,y,z range (A): 47.09500 45.30600 60.92800 scale (grids/A): 1.752889 object centre (A): 21.30350 7.285000 11.22200 number of atom coordinates read : 2362 total number of charged atoms : 2285 net assigned charge : 4.000001 assigned positive charge : 351.5241 centred at (gu) : 91.88792 86.17572 86.86904 assigned negative charge : -347.5247 centred at (gu) : 92.00455 86.54916 86.94059 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 57775 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20530 grid for indexing accessible points = 1.400000 m= 18346 mr = 39613 m= 2320 mr = 13004 m= 73 mr = 1381 m= 0 mr = 7 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 995 time to turn everything in is 0.5100000 number of dielectric boundary points 24509 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 173 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 17740 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) : 0.5842962 object centre at (A) : 21.30350 7.285000 11.22200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6936049E-02 1.3086307E-02 midg,1,midg; midg,igrid,midg 1.3061689E-02 -2.6660506E-03 1,midg,midg; igrid,midg,midg 3.6718554E-03 -1.6242906E-02 gauss-seidel spectral radius is 0.9983614 estimated iterations to convergence 196 setup time was (sec) 0.8200000 now iterating at: 15:55:33 rms-change max change #iterations 3.348353 153.4850 at 10iterations 1.463766 52.28633 at 20iterations 0.6386207 23.11433 at 30iterations 0.2796610 10.58024 at 40iterations 0.1219484 4.349024 at 50iterations 5.3268321E-02 2.143038 at 60iterations 2.3364346E-02 0.8211927 at 70iterations 1.0147352E-02 0.3997154 at 80iterations 4.4338242E-03 0.1596413 at 90iterations 1.9395974E-03 7.0354462E-02 at 100iterations 8.5529475E-04 2.9586792E-02 at 110iterations 3.7711006E-04 1.3486862E-02 at 120iterations finished qdiffx linear iterations at : 15:55:42 total time elapsed so far: 9.350000 # loops : 120 mean,max change (kT/e) : 3.7711006E-04 1.3486862E-02 energy calculations done at 9.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.530000 DelPhi exited at 15:55:42 9.529u 0.351s 0:10.17 97.0% 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 15:55:42 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2362 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: 2.629333 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): -2.244000 44.85100 ymin,ymax (A): -15.36800 29.93800 zmin,zma (A): -19.24200 41.68600 x,y,z range (A): 47.09500 45.30600 60.92800 scale (grids/A): 2.629333 object centre (A): 21.30350 7.285000 11.22200 number of atom coordinates read : 2362 total number of charged atoms : 2285 net assigned charge : 4.000001 assigned positive charge : 351.5241 centred at (gu) : 92.83168 84.26351 85.30351 assigned negative charge : -347.5247 centred at (gu) : 93.00674 84.82370 85.41093 start vw surface at 0.1500000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 134312 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20530 grid for indexing accessible points = 1.400000 m= 62254 mr = 96917 m= 19638 mr = 49789 m= 3882 mr = 15389 m= 321 mr = 2896 m= 11 mr = 175 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 3451 time to turn everything in is 1.290000 number of dielectric boundary points 55252 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 18272 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) : 1.752889 object centre at (A) : 21.30350 7.285000 11.22200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2303664 0.3952628 midg,1,midg; midg,igrid,midg 0.1380804 -3.3367250E-02 1,midg,midg; igrid,midg,midg 5.1567715E-02 -0.2541411 gauss-seidel spectral radius is 0.9991758 estimated iterations to convergence 275 setup time was (sec) 1.620000 now iterating at: 15:55:44 rms-change max change #iterations 8.323318 290.9911 at 10iterations 4.723735 123.5734 at 20iterations 2.666896 63.86991 at 30iterations 1.503561 33.61395 at 40iterations 0.8453652 19.52497 at 50iterations 0.4753109 10.30288 at 60iterations 0.2662105 5.582926 at 70iterations 0.1492116 3.143436 at 80iterations 8.3336532E-02 2.195827 at 90iterations 4.6444453E-02 0.9189413 at 100iterations 2.6039816E-02 0.5545597 at 110iterations 1.4535033E-02 0.3345277 at 120iterations 8.1155933E-03 0.1607320 at 130iterations 4.5241080E-03 9.7358704E-02 at 140iterations 2.5279543E-03 6.5870285E-02 at 150iterations 1.4116921E-03 3.2025337E-02 at 160iterations 7.9160329E-04 1.7856598E-02 at 170iterations 4.4542048E-04 8.8510513E-03 at 180iterations finished qdiffx linear iterations at : 15:55:58 total time elapsed so far: 15.46000 # loops : 180 mean,max change (kT/e) : 4.4542048E-04 8.8510513E-03 energy calculations done at 15.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.64000 DelPhi exited at 15:55:59 15.639u 0.362s 0:16.29 98.1% 0+0k 0+0io 0pf+0w