Sun Oct 9 07:21:27 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 Sun Oct 9 2011 at 07:21:27 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 = 2496 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: 0.5434949 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): -4.243000 41.97600 ymin,ymax (A): 35.80600 87.32500 zmin,zma (A): -3.932000 61.57000 x,y,z range (A): 46.21900 51.51900 65.50200 scale (grids/A): 0.5434949 object centre (A): 18.86650 61.56550 28.81900 number of atom coordinates read : 2496 total number of charged atoms : 2351 net assigned charge : -10.49998 assigned positive charge : 373.7270 centred at (gu) : 90.61066 89.05820 89.67159 assigned negative charge : -384.2274 centred at (gu) : 90.76955 88.69479 89.57973 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 4778 nv = 96 ne = 84 npr = 49971 no. pairs analyzed = 49971 no. exposed pairs = 3536 no. arc points = 25351 no. surface atoms = 1185 nbur = 1311 mkacc time = 0.1100000 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 = 1.568000 m= 186 mr = 2172 m= 0 mr = 4 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2788 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2542 ## 336 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 6261 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1331580E-09 -8.1299814E-11 midg,1,midg; midg,igrid,midg -3.2288709E-09 9.8374930E-10 1,midg,midg; igrid,midg,midg 2.1326815E-10 -1.6369968E-09 gauss-seidel spectral radius is 0.9825172 estimated iterations to convergence 62 setup time was (sec) 0.5400000 now iterating at: 07:21:28 rms-change max change #iterations 6.2573813E-02 13.77540 at 10iterations 3.9300337E-03 0.7995567 at 20iterations 2.6447780E-04 4.9886703E-02 at 30iterations 1.7619013E-05 3.2806396E-03 at 40iterations 1.2154964E-06 2.1171570E-04 at 50iterations finished qdiffx linear iterations at : 07:21:31 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 1.2154964E-06 2.1171570E-04 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 07:21:31 3.544u 0.201s 0:04.02 93.0% 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 Sun Oct 9 2011 at 07:21:31 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 = 2496 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: 1.630485 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): -4.243000 41.97600 ymin,ymax (A): 35.80600 87.32500 zmin,zma (A): -3.932000 61.57000 x,y,z range (A): 46.21900 51.51900 65.50200 scale (grids/A): 1.630485 object centre (A): 18.86650 61.56550 28.81900 number of atom coordinates read : 2496 total number of charged atoms : 2351 net assigned charge : -10.49998 assigned positive charge : 373.7270 centred at (gu) : 91.83167 87.17416 89.01407 assigned negative charge : -384.2274 centred at (gu) : 92.30831 86.08417 88.73886 start vw surface at 0.1500000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 52933 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25351 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 15182 mr = 33122 m= 1331 mr = 9863 m= 33 mr = 542 m= 2 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 86 time to turn everything in is 0.4300000 number of dielectric boundary points 25949 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 304 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 17993 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) : 0.5434949 object centre at (A) : 18.86650 61.56550 28.81900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3655081E-02 5.9998711E-03 midg,1,midg; midg,igrid,midg -2.2543743E-02 6.7981612E-03 1,midg,midg; igrid,midg,midg -2.8962067E-03 -1.5356507E-02 gauss-seidel spectral radius is 0.9981273 estimated iterations to convergence 184 setup time was (sec) 0.7400000 now iterating at: 07:21:32 rms-change max change #iterations 2.991116 190.9164 at 10iterations 1.225960 52.29663 at 20iterations 0.5016940 21.16182 at 30iterations 0.2063223 7.492424 at 40iterations 8.4615082E-02 3.364976 at 50iterations 3.4754921E-02 1.470657 at 60iterations 1.4182596E-02 0.5713615 at 70iterations 5.8392012E-03 0.2278190 at 80iterations 2.3932480E-03 9.5458031E-02 at 90iterations 9.8444882E-04 3.7073135E-02 at 100iterations 4.0433111E-04 1.5946388E-02 at 110iterations 1.6632212E-04 6.6022873E-03 at 120iterations finished qdiffx linear iterations at : 07:21:39 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 1.6632212E-04 6.6022873E-03 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 07:21:40 7.907u 0.217s 0:08.40 96.5% 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 07:21:40 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 = 2496 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: 2.445727 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): -4.243000 41.97600 ymin,ymax (A): 35.80600 87.32500 zmin,zma (A): -3.932000 61.57000 x,y,z range (A): 46.21900 51.51900 65.50200 scale (grids/A): 2.445727 object centre (A): 18.86650 61.56550 28.81900 number of atom coordinates read : 2496 total number of charged atoms : 2351 net assigned charge : -10.49998 assigned positive charge : 373.7270 centred at (gu) : 92.74741 85.76109 88.52108 assigned negative charge : -384.2274 centred at (gu) : 93.46243 84.12611 88.10822 start vw surface at 0.1500000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 122306 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25351 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 53325 mr = 81358 m= 13725 mr = 40626 m= 1941 mr = 9725 m= 97 mr = 1135 m= 0 mr = 39 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 332 time to turn everything in is 1.000000 number of dielectric boundary points 58511 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 18789 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) : 1.630485 object centre at (A) : 18.86650 61.56550 28.81900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8369417 6.7237042E-02 midg,1,midg; midg,igrid,midg -0.3038244 9.7839564E-02 1,midg,midg; igrid,midg,midg -4.2897046E-02 -0.1966241 gauss-seidel spectral radius is 0.9991118 estimated iterations to convergence 265 setup time was (sec) 1.320000 now iterating at: 07:21:41 rms-change max change #iterations 7.875420 314.9951 at 10iterations 4.364322 117.4492 at 20iterations 2.423157 64.02399 at 30iterations 1.336392 37.63978 at 40iterations 0.7366309 18.88159 at 50iterations 0.4036657 10.21859 at 60iterations 0.2208251 5.313652 at 70iterations 0.1206162 2.861090 at 80iterations 6.6017278E-02 1.506140 at 90iterations 3.6024421E-02 0.8523254 at 100iterations 1.9627577E-02 0.4508712 at 110iterations 1.0712955E-02 0.2543259 at 120iterations 5.8358442E-03 0.1420069 at 130iterations 3.1839616E-03 7.3152542E-02 at 140iterations 1.7307582E-03 4.0334702E-02 at 150iterations 9.4228826E-04 2.4269104E-02 at 160iterations 5.1153568E-04 1.0887146E-02 at 170iterations 2.7900783E-04 7.6918602E-03 at 180iterations finished qdiffx linear iterations at : 07:21:52 total time elapsed so far: 12.22000 # loops : 180 mean,max change (kT/e) : 2.7900783E-04 7.6918602E-03 energy calculations done at 12.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.40000 DelPhi exited at 07:21:53 12.405u 0.231s 0:12.96 97.4% 0+0k 0+0io 0pf+0w