Mon Oct 10 11:34:56 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 Mon Oct 10 2011 at 11:34:56 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: ASL 51 has a net charge of -0.1000 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 0.7402324 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): 8.350000 56.44300 ymin,ymax (A): -9.050000 36.47600 zmin,zma (A): -3.021000 44.31500 x,y,z range (A): 48.09300 45.52600 47.33600 scale (grids/A): 0.7402324 object centre (A): 32.39650 13.71300 20.64700 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.371980 assigned positive charge : 319.7998 centred at (gu) : 89.66660 90.52920 89.83615 assigned negative charge : -326.1720 centred at (gu) : 89.67487 90.60154 90.04160 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8046 nv = 96 ne = 84 npr = 43229 no. pairs analyzed = 43229 no. exposed pairs = 2672 no. arc points = 18948 no. surface atoms = 905 nbur = 1212 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 568 mr = 4506 m= 5 mr = 126 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 66 time to turn everything in is 0.2500000 number of dielectric boundary points 3987 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1527 ## 122 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 8441 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0031174E-07 -3.2055934E-07 midg,1,midg; midg,igrid,midg -3.4834990E-08 -2.0779335E-07 1,midg,midg; igrid,midg,midg -1.1038209E-07 -1.1411921E-07 gauss-seidel spectral radius is 0.9904919 estimated iterations to convergence 83 setup time was (sec) 0.4600000 now iterating at: 11:34:57 rms-change max change #iterations 0.2511875 34.37495 at 10iterations 3.4174312E-02 4.669598 at 20iterations 4.5604655E-03 0.5506439 at 30iterations 6.1610073E-04 7.6116562E-02 at 40iterations 8.3473926E-05 9.8104477E-03 at 50iterations finished qdiffx linear iterations at : 11:34:59 total time elapsed so far: 3.070000 # loops : 50 mean,max change (kT/e) : 8.3473926E-05 9.8104477E-03 energy calculations done at 3.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 11:35:00 3.234u 0.256s 0:03.78 92.0% 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 Mon Oct 10 2011 at 11:35:00 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: ASL 51 has a net charge of -0.1000 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 2.220697 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): 8.350000 56.44300 ymin,ymax (A): -9.050000 36.47600 zmin,zma (A): -3.021000 44.31500 x,y,z range (A): 48.09300 45.52600 47.33600 scale (grids/A): 2.220697 object centre (A): 32.39650 13.71300 20.64700 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.371980 assigned positive charge : 319.7998 centred at (gu) : 88.99961 91.58747 89.50809 assigned negative charge : -326.1720 centred at (gu) : 89.02461 91.80434 90.12488 start vw surface at 0.1200000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 84753 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18948 grid for indexing accessible points = 1.400000 m= 34132 mr = 58777 m= 7418 mr = 26170 m= 838 mr = 5197 m= 29 mr = 489 m= 0 mr = 1 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1590 time to turn everything in is 0.5900000 number of dielectric boundary points 36536 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 41 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 15752 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) : 0.7402324 object centre at (A) : 32.39650 13.71300 20.64700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.7939808E-03 -0.1258474 midg,1,midg; midg,igrid,midg -3.2087900E-02 -4.4244032E-02 1,midg,midg; igrid,midg,midg 4.5548496E-03 4.4428227E-03 gauss-seidel spectral radius is 0.9989284 estimated iterations to convergence 242 setup time was (sec) 0.8800000 now iterating at: 11:35:01 rms-change max change #iterations 5.184920 232.5269 at 10iterations 2.631515 76.27325 at 20iterations 1.344845 37.12313 at 30iterations 0.6856419 19.27054 at 40iterations 0.3497351 9.554147 at 50iterations 0.1780001 4.717546 at 60iterations 9.0754069E-02 2.745571 at 70iterations 4.6514384E-02 1.353996 at 80iterations 2.3709269E-02 0.6878014 at 90iterations 1.2082681E-02 0.3779488 at 100iterations 6.1659962E-03 0.1791102 at 110iterations 3.1583202E-03 9.5432281E-02 at 120iterations finished qdiffx linear iterations at : 11:35:08 total time elapsed so far: 8.260000 # loops : 120 mean,max change (kT/e) : 3.1583202E-03 9.5432281E-02 energy calculations done at 8.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.430000 DelPhi exited at 11:35:09 8.430u 0.267s 0:09.04 96.1% 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 Mon Oct 10 2011 at 11:35:09 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: ASL 51 has a net charge of -0.1000 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 3.331046 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): 8.350000 56.44300 ymin,ymax (A): -9.050000 36.47600 zmin,zma (A): -3.021000 44.31500 x,y,z range (A): 48.09300 45.52600 47.33600 scale (grids/A): 3.331046 object centre (A): 32.39650 13.71300 20.64700 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.371980 assigned positive charge : 319.7998 centred at (gu) : 88.49929 92.38113 89.26207 assigned negative charge : -326.1720 centred at (gu) : 88.53695 92.70646 90.18732 start vw surface at 0.1200000 fill in re-entrant regions at 0.8700000 boundary points on vw surface= 194920 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18948 grid for indexing accessible points = 1.400000 m= 104222 mr = 141199 m= 45035 mr = 86769 m= 14254 mr = 37581 m= 3343 mr = 11385 m= 501 mr = 2635 m= 26 mr = 327 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.9399999 no. cavity mid-points inaccessible to solvent = 5408 time to turn everything in is 1.950000 number of dielectric boundary points 82396 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.090000 number of grid points assigned charge 15824 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) : 2.220697 object centre at (A) : 32.39650 13.71300 20.64700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1715405 -1.190742 midg,1,midg; midg,igrid,midg -0.2853511 -0.2476983 1,midg,midg; igrid,midg,midg 2.0179646E-02 4.5012258E-02 gauss-seidel spectral radius is 0.9993181 estimated iterations to convergence 302 setup time was (sec) 2.270000 now iterating at: 11:35:11 rms-change max change #iterations 11.12526 387.2011 at 10iterations 6.556348 140.8473 at 20iterations 3.868830 67.80950 at 30iterations 2.270043 45.06213 at 40iterations 1.335737 22.83642 at 50iterations 0.7874446 12.96187 at 60iterations 0.4620647 7.581238 at 70iterations 0.2705027 4.489273 at 80iterations 0.1592867 2.679293 at 90iterations 9.3652546E-02 1.485241 at 100iterations 5.4955382E-02 1.022758 at 110iterations 3.2254390E-02 0.5805330 at 120iterations 1.8934248E-02 0.3176365 at 130iterations 1.1131487E-02 0.1779135 at 140iterations 6.5370318E-03 0.1053324 at 150iterations 3.8358795E-03 6.6062123E-02 at 160iterations 2.2526542E-03 3.6876678E-02 at 170iterations 1.3228406E-03 2.1526337E-02 at 180iterations finished qdiffx linear iterations at : 11:35:21 total time elapsed so far: 12.19000 # loops : 180 mean,max change (kT/e) : 1.3228406E-03 2.1526337E-02 energy calculations done at 12.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.38000 DelPhi exited at 11:35:22 12.383u 0.277s 0:13.00 97.3% 0+0k 0+0io 0pf+0w