Sun Oct 9 14:43:35 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 Sun Oct 9 2011 at 14:43:35 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 = 2499 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: 0.5407376 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): -20.15000 45.68600 ymin,ymax (A): -24.20400 28.04300 zmin,zma (A): -10.09900 37.66100 x,y,z range (A): 65.83600 52.24700 47.76000 scale (grids/A): 0.5407376 object centre (A): 12.76800 1.919500 13.78100 number of atom coordinates read : 2499 total number of charged atoms : 2359 net assigned charge : 8.000021 assigned positive charge : 376.5219 centred at (gu) : 89.50552 90.18810 90.65295 assigned negative charge : -368.5225 centred at (gu) : 89.22318 90.30112 90.68526 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 4908 nv = 96 ne = 84 npr = 46195 no. pairs analyzed = 46195 no. exposed pairs = 3725 no. arc points = 27260 no. surface atoms = 1238 nbur = 1261 mkacc time = 9.9999994E-02 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 = 1.596000 m= 189 mr = 2128 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 2969 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2722 ## 394 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 6357 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7888782E-10 3.1512198E-10 midg,1,midg; midg,igrid,midg 8.7770075E-10 -1.0738747E-10 1,midg,midg; igrid,midg,midg -1.0304088E-09 1.4555021E-09 gauss-seidel spectral radius is 0.9823487 estimated iterations to convergence 62 setup time was (sec) 0.4600000 now iterating at: 14:43:36 rms-change max change #iterations 6.1848786E-02 10.39966 at 10iterations 3.9381511E-03 0.7587872 at 20iterations 2.7112919E-04 4.7266006E-02 at 30iterations 2.3275907E-05 3.3836365E-03 at 40iterations 3.0711346E-06 4.7683716E-04 at 50iterations finished qdiffx linear iterations at : 14:43:38 total time elapsed so far: 2.870000 # loops : 50 mean,max change (kT/e) : 3.0711346E-06 4.7683716E-04 energy calculations done at 2.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.030000 DelPhi exited at 14:43:39 3.038u 0.155s 0:03.46 91.9% 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 14:43:39 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 = 2499 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: 1.622213 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): -20.15000 45.68600 ymin,ymax (A): -24.20400 28.04300 zmin,zma (A): -10.09900 37.66100 x,y,z range (A): 65.83600 52.24700 47.76000 scale (grids/A): 1.622213 object centre (A): 12.76800 1.919500 13.78100 number of atom coordinates read : 2499 total number of charged atoms : 2359 net assigned charge : 8.000021 assigned positive charge : 376.5219 centred at (gu) : 88.51598 90.56368 91.95863 assigned negative charge : -368.5225 centred at (gu) : 87.66927 90.90318 92.05563 start vw surface at 0.1500000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 53821 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27260 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 14559 mr = 32856 m= 1287 mr = 8783 m= 36 mr = 446 m= 0 mr = 2 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 27616 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 351 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 18019 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) : 0.5407376 object centre at (A) : 12.76800 1.919500 13.78100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.6653335E-03 8.0404534E-05 midg,1,midg; midg,igrid,midg 1.1676309E-02 -3.2059157E-03 1,midg,midg; igrid,midg,midg -3.7197769E-02 2.4210084E-02 gauss-seidel spectral radius is 0.9981294 estimated iterations to convergence 184 setup time was (sec) 0.6500000 now iterating at: 14:43:40 rms-change max change #iterations 2.936167 150.2350 at 10iterations 1.200834 55.86416 at 20iterations 0.4895782 19.76188 at 30iterations 0.2003250 7.974119 at 40iterations 8.2065955E-02 3.602814 at 50iterations 3.3698961E-02 1.395650 at 60iterations 1.3756245E-02 0.5556107 at 70iterations 5.6219902E-03 0.2290573 at 80iterations 2.3142765E-03 9.6208572E-02 at 90iterations 9.5422927E-04 4.0200233E-02 at 100iterations 3.9141616E-04 1.6761303E-02 at 110iterations 1.6100638E-04 6.7062378E-03 at 120iterations finished qdiffx linear iterations at : 14:43:45 total time elapsed so far: 6.500000 # loops : 120 mean,max change (kT/e) : 1.6100638E-04 6.7062378E-03 energy calculations done at 6.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.670000 DelPhi exited at 14:43:46 6.673u 0.145s 0:07.15 95.2% 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 14:43:46 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 = 2499 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: 2.433319 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): -20.15000 45.68600 ymin,ymax (A): -24.20400 28.04300 zmin,zma (A): -10.09900 37.66100 x,y,z range (A): 65.83600 52.24700 47.76000 scale (grids/A): 2.433319 object centre (A): 12.76800 1.919500 13.78100 number of atom coordinates read : 2499 total number of charged atoms : 2359 net assigned charge : 8.000021 assigned positive charge : 376.5219 centred at (gu) : 87.77382 90.84539 92.93779 assigned negative charge : -368.5225 centred at (gu) : 86.50391 91.35471 93.08337 start vw surface at 0.1500000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 124904 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27260 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 51783 mr = 81672 m= 12705 mr = 37920 m= 1712 mr = 8397 m= 117 mr = 913 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8900000 number of dielectric boundary points 62284 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 18849 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) : 1.622213 object centre at (A) : 12.76800 1.919500 13.78100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1289012 -1.3855410E-02 midg,1,midg; midg,igrid,midg 0.1814888 -4.4711843E-02 1,midg,midg; igrid,midg,midg -0.6000715 0.2602668 gauss-seidel spectral radius is 0.9991183 estimated iterations to convergence 266 setup time was (sec) 1.160000 now iterating at: 14:43:47 rms-change max change #iterations 7.859354 395.5377 at 10iterations 4.446652 133.9462 at 20iterations 2.494902 72.27718 at 30iterations 1.383051 35.71240 at 40iterations 0.7646760 19.98235 at 50iterations 0.4215054 11.12301 at 60iterations 0.2311782 5.855316 at 70iterations 0.1267608 3.532185 at 80iterations 6.9426045E-02 1.707314 at 90iterations 3.8046136E-02 0.9317484 at 100iterations 2.0752417E-02 0.4893566 at 110iterations 1.1327702E-02 0.2586994 at 120iterations 6.1903554E-03 0.1493454 at 130iterations 3.3829175E-03 8.0775261E-02 at 140iterations 1.8383613E-03 3.9371490E-02 at 150iterations 1.0033859E-03 2.2031784E-02 at 160iterations 5.4792594E-04 1.2050629E-02 at 170iterations 2.9898915E-04 7.2364807E-03 at 180iterations finished qdiffx linear iterations at : 14:43:57 total time elapsed so far: 10.39000 # loops : 180 mean,max change (kT/e) : 2.9898915E-04 7.2364807E-03 energy calculations done at 10.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.56000 DelPhi exited at 14:43:57 10.561u 0.160s 0:11.08 96.7% 0+0k 0+0io 0pf+0w