Sun Oct 9 10:57:07 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 10:57:07 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 = 2615 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6045169 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): -21.82300 37.06700 ymin,ymax (A): 18.63300 75.75800 zmin,zma (A): 36.18900 88.57100 x,y,z range (A): 58.89000 57.12500 52.38200 scale (grids/A): 0.6045169 object centre (A): 7.621999 47.19550 62.38000 number of atom coordinates read : 2615 total number of charged atoms : 2472 net assigned charge : -7.499968 assigned positive charge : 375.1845 centred at (gu) : 90.02728 86.94765 89.93364 assigned negative charge : -382.6858 centred at (gu) : 90.10441 87.13751 90.14539 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6592 nv = 96 ne = 84 npr = 52189 no. pairs analyzed = 52189 no. exposed pairs = 3598 no. arc points = 25447 no. surface atoms = 1209 nbur = 1406 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 347 mr = 3302 m= 4 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3606 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2408 ## 199 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7979 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6038280E-09 -1.2623885E-08 midg,1,midg; midg,igrid,midg 7.7733713E-09 -6.0299530E-09 1,midg,midg; igrid,midg,midg -7.9683121E-10 -7.1605988E-09 gauss-seidel spectral radius is 0.9858525 estimated iterations to convergence 69 setup time was (sec) 0.3800000 now iterating at: 10:57:08 rms-change max change #iterations 0.1090367 16.40244 at 10iterations 9.4261300E-03 1.665508 at 20iterations 8.1430929E-04 0.1120243 at 30iterations 7.4661461E-05 1.1451721E-02 at 40iterations 9.4377119E-06 1.8234253E-03 at 50iterations finished qdiffx linear iterations at : 10:57:11 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 9.4377119E-06 1.8234253E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 10:57:11 3.356u 0.185s 0:03.82 92.4% 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 10:57:11 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 = 2615 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.813551 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): -21.82300 37.06700 ymin,ymax (A): 18.63300 75.75800 zmin,zma (A): 36.18900 88.57100 x,y,z range (A): 58.89000 57.12500 52.38200 scale (grids/A): 1.813551 object centre (A): 7.621999 47.19550 62.38000 number of atom coordinates read : 2615 total number of charged atoms : 2472 net assigned charge : -7.499968 assigned positive charge : 375.1845 centred at (gu) : 90.08131 80.84264 89.80031 assigned negative charge : -382.6858 centred at (gu) : 90.31320 81.41248 90.43606 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 71481 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25447 grid for indexing accessible points = 1.400000 m= 23979 mr = 47232 m= 3632 mr = 16674 m= 194 mr = 2109 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 664 time to turn everything in is 0.3500000 number of dielectric boundary points 33227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 162 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 19378 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) : 0.6045169 object centre at (A) : 7.621999 47.19550 62.38000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1057433E-02 -3.7116855E-02 midg,1,midg; midg,igrid,midg 1.9286945E-02 -4.7964115E-02 1,midg,midg; igrid,midg,midg -2.0611878E-02 -2.7908597E-02 gauss-seidel spectral radius is 0.9985182 estimated iterations to convergence 206 setup time was (sec) 0.5700000 now iterating at: 10:57:12 rms-change max change #iterations 3.787210 169.8378 at 10iterations 1.706483 66.63370 at 20iterations 0.7710145 26.69998 at 30iterations 0.3509250 11.34212 at 40iterations 0.1579001 5.492592 at 50iterations 7.1775630E-02 2.422813 at 60iterations 3.2466326E-02 1.039482 at 70iterations 1.4736908E-02 0.4661491 at 80iterations 6.7131324E-03 0.2153015 at 90iterations 3.0324343E-03 0.1142635 at 100iterations 1.3737156E-03 4.4506073E-02 at 110iterations 6.2673260E-04 2.0858765E-02 at 120iterations finished qdiffx linear iterations at : 10:57:19 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 6.2673260E-04 2.0858765E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 10:57:20 7.865u 0.221s 0:08.50 95.0% 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 10:57:20 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 = 2615 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.720326 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): -21.82300 37.06700 ymin,ymax (A): 18.63300 75.75800 zmin,zma (A): 36.18900 88.57100 x,y,z range (A): 58.89000 57.12500 52.38200 scale (grids/A): 2.720326 object centre (A): 7.621999 47.19550 62.38000 number of atom coordinates read : 2615 total number of charged atoms : 2472 net assigned charge : -7.499968 assigned positive charge : 375.1845 centred at (gu) : 90.12173 76.26382 89.70036 assigned negative charge : -382.6858 centred at (gu) : 90.46958 77.11861 90.65401 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 165431 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25447 grid for indexing accessible points = 1.400000 m= 77904 mr = 115640 m= 27289 mr = 61165 m= 6393 mr = 21048 m= 816 mr = 4493 m= 37 mr = 468 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 2186 time to turn everything in is 0.8900000 number of dielectric boundary points 75047 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 19773 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) : 1.813551 object centre at (A) : 7.621999 47.19550 62.38000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2693204 -0.3654273 midg,1,midg; midg,igrid,midg 0.3061179 -0.7313456 1,midg,midg; igrid,midg,midg -0.3399647 -0.3003696 gauss-seidel spectral radius is 0.9992365 estimated iterations to convergence 286 setup time was (sec) 1.120000 now iterating at: 10:57:21 rms-change max change #iterations 9.299124 304.7443 at 10iterations 5.450409 133.6141 at 20iterations 3.156930 63.60200 at 30iterations 1.822056 36.08900 at 40iterations 1.050157 20.18624 at 50iterations 0.6032540 11.68559 at 60iterations 0.3453407 6.615409 at 70iterations 0.1976915 3.948857 at 80iterations 0.1128860 2.131882 at 90iterations 6.4436957E-02 1.262278 at 100iterations 3.6831230E-02 0.6624165 at 110iterations 2.0954927E-02 0.4016876 at 120iterations 1.1967190E-02 0.2246399 at 130iterations 6.8205888E-03 0.1279440 at 140iterations 3.8906690E-03 7.3822975E-02 at 150iterations 2.2192013E-03 4.0797710E-02 at 160iterations 1.2619867E-03 2.3488045E-02 at 170iterations 7.2213076E-04 1.3226509E-02 at 180iterations finished qdiffx linear iterations at : 10:57:33 total time elapsed so far: 12.61000 # loops : 180 mean,max change (kT/e) : 7.2213076E-04 1.3226509E-02 energy calculations done at 12.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.75000 DelPhi exited at 10:57:33 12.751u 0.211s 0:13.22 98.0% 0+0k 0+0io 0pf+0w