Tue Oct 11 06:59:56 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 Tue Oct 11 2011 at 06:59:56 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3012 !!! WARNING: UMP 317 has a net charge of -0.1000 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: 0.5915193 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): -15.59900 44.58500 ymin,ymax (A): 19.40700 77.13000 zmin,zma (A): -70.29700 -21.57600 x,y,z range (A): 60.18400 57.72300 48.72100 scale (grids/A): 0.5915193 object centre (A): 14.49300 48.26850 -45.93650 number of atom coordinates read : 3012 total number of charged atoms : 2869 net assigned charge : -4.099988 assigned positive charge : 438.9295 centred at (gu) : 89.26495 89.73868 90.31867 assigned negative charge : -443.0299 centred at (gu) : 89.26414 89.97183 90.29027 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6902 nv = 96 ne = 84 npr = 63572 no. pairs analyzed = 63572 no. exposed pairs = 3777 no. arc points = 26160 no. surface atoms = 1282 nbur = 1730 mkacc time = 0.1700000 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= 344 mr = 3749 m= 0 mr = 39 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3458 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2593 ## 288 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8758 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0946784E-09 -4.6762483E-10 midg,1,midg; midg,igrid,midg 6.2754406E-09 -8.4599590E-09 1,midg,midg; igrid,midg,midg -1.6127488E-09 -1.1187452E-09 gauss-seidel spectral radius is 0.9852467 estimated iterations to convergence 68 setup time was (sec) 0.6800000 now iterating at: 06:59:57 rms-change max change #iterations 0.1072598 16.58935 at 10iterations 8.9872917E-03 1.565801 at 20iterations 7.4317801E-04 0.1177254 at 30iterations 6.6469940E-05 1.0265350E-02 at 40iterations 8.7738381E-06 1.6746521E-03 at 50iterations finished qdiffx linear iterations at : 07:00:01 total time elapsed so far: 4.070000 # loops : 50 mean,max change (kT/e) : 8.7738381E-06 1.6746521E-03 energy calculations done at 4.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.250000 DelPhi exited at 07:00:01 4.255u 0.238s 0:04.94 90.6% 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 Tue Oct 11 2011 at 07:00:01 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3012 !!! WARNING: UMP 317 has a net charge of -0.1000 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: 1.774558 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): -15.59900 44.58500 ymin,ymax (A): 19.40700 77.13000 zmin,zma (A): -70.29700 -21.57600 x,y,z range (A): 60.18400 57.72300 48.72100 scale (grids/A): 1.774558 object centre (A): 14.49300 48.26850 -45.93650 number of atom coordinates read : 3012 total number of charged atoms : 2869 net assigned charge : -4.099988 assigned positive charge : 438.9295 centred at (gu) : 87.79461 89.21545 90.95541 assigned negative charge : -443.0299 centred at (gu) : 87.79203 89.91530 90.87048 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 74695 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26160 grid for indexing accessible points = 1.400000 m= 26365 mr = 51216 m= 3969 mr = 19393 m= 167 mr = 2562 m= 1 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 753 time to turn everything in is 0.6600000 number of dielectric boundary points 31977 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 192 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 22353 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) : 0.5915193 object centre at (A) : 14.49300 48.26850 -45.93650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4565980E-03 2.0536944E-02 midg,1,midg; midg,igrid,midg 4.5146924E-03 -2.6625095E-02 1,midg,midg; igrid,midg,midg -2.8748047E-02 -2.4928518E-02 gauss-seidel spectral radius is 0.9984750 estimated iterations to convergence 203 setup time was (sec) 0.9700000 now iterating at: 07:00:03 rms-change max change #iterations 3.944654 204.9232 at 10iterations 1.769874 55.95843 at 20iterations 0.7958097 26.72507 at 30iterations 0.3566602 14.61566 at 40iterations 0.1602574 5.667079 at 50iterations 7.1831353E-02 2.448201 at 60iterations 3.2278780E-02 0.9442673 at 70iterations 1.4439355E-02 0.4607115 at 80iterations 6.4981305E-03 0.2151260 at 90iterations 2.9231578E-03 9.6736908E-02 at 100iterations 1.3140596E-03 4.0176392E-02 at 110iterations 5.9145520E-04 1.6802311E-02 at 120iterations finished qdiffx linear iterations at : 07:00:11 total time elapsed so far: 9.390000 # loops : 120 mean,max change (kT/e) : 5.9145520E-04 1.6802311E-02 energy calculations done at 9.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.580000 DelPhi exited at 07:00:12 9.581u 0.287s 0:10.17 96.9% 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 Tue Oct 11 2011 at 07:00:12 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3012 !!! WARNING: UMP 317 has a net charge of -0.1000 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: 2.661837 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): -15.59900 44.58500 ymin,ymax (A): 19.40700 77.13000 zmin,zma (A): -70.29700 -21.57600 x,y,z range (A): 60.18400 57.72300 48.72100 scale (grids/A): 2.661837 object centre (A): 14.49300 48.26850 -45.93650 number of atom coordinates read : 3012 total number of charged atoms : 2869 net assigned charge : -4.099988 assigned positive charge : 438.9295 centred at (gu) : 86.69156 88.82301 91.43282 assigned negative charge : -443.0299 centred at (gu) : 86.68810 89.87280 91.30559 start vw surface at 0.1600000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 172854 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26160 grid for indexing accessible points = 1.400000 m= 85613 mr = 124697 m= 30605 mr = 69419 m= 7036 mr = 24718 m= 843 mr = 5403 m= 44 mr = 563 m= 0 mr = 17 time to grow re-entrant surface = 0.8500001 no. cavity mid-points inaccessible to solvent = 2758 time to turn everything in is 1.460000 number of dielectric boundary points 72178 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 22948 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) : 1.774558 object centre at (A) : 14.49300 48.26850 -45.93650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.7499199E-02 0.3391995 midg,1,midg; midg,igrid,midg -2.0588990E-02 -0.1931823 1,midg,midg; igrid,midg,midg -0.3230198 -0.3252773 gauss-seidel spectral radius is 0.9992297 estimated iterations to convergence 284 setup time was (sec) 1.800000 now iterating at: 07:00:14 rms-change max change #iterations 9.747147 315.3092 at 10iterations 5.672752 128.6736 at 20iterations 3.279234 80.24715 at 30iterations 1.884728 38.77753 at 40iterations 1.078731 22.05396 at 50iterations 0.6182615 12.84924 at 60iterations 0.3528462 7.068325 at 70iterations 0.2014565 4.037621 at 80iterations 0.1145210 2.240988 at 90iterations 6.5342471E-02 1.175340 at 100iterations 3.7070654E-02 0.6605116 at 110iterations 2.1115985E-02 0.4881237 at 120iterations 1.1999974E-02 0.2141418 at 130iterations 6.8039978E-03 0.1297259 at 140iterations 3.8620890E-03 7.7373505E-02 at 150iterations 2.1943694E-03 3.8567126E-02 at 160iterations 1.2488798E-03 2.5508881E-02 at 170iterations 7.0869346E-04 1.3351440E-02 at 180iterations finished qdiffx linear iterations at : 07:00:27 total time elapsed so far: 15.34000 # loops : 180 mean,max change (kT/e) : 7.0869346E-04 1.3351440E-02 energy calculations done at 15.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.52000 DelPhi exited at 07:00:28 15.517u 0.279s 0:16.15 97.7% 0+0k 0+0io 0pf+0w