Mon Oct 10 17:03:06 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 17:03:06 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1361 !!! WARNING: HIT 6 has a net charge of 0.5140 !!! WARNING: HIT 27 has a net charge of 0.5140 !!! WARNING: HIR 47 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7473809 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): 34.63600 82.26900 ymin,ymax (A): 10.92200 52.35900 zmin,zma (A): 25.47000 60.31000 x,y,z range (A): 47.63301 41.43700 34.84000 scale (grids/A): 0.7473809 object centre (A): 58.45250 31.64050 42.89000 number of atom coordinates read : 1361 total number of charged atoms : 1238 net assigned charge : 16.04199 assigned positive charge : 213.3342 centred at (gu) : 90.33339 90.32773 88.63270 assigned negative charge : -197.2922 centred at (gu) : 90.46884 90.25875 88.58710 start vw surface at 5.9999999E-02 fill in re-entrant regions at 5.9999999E-02 boundary points on vw surface= 4853 nv = 96 ne = 84 npr = 27495 no. pairs analyzed = 27495 no. exposed pairs = 1636 no. arc points = 12008 no. surface atoms = 559 nbur = 802 mkacc time = 3.9999999E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 360 mr = 2532 m= 5 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 4.9999997E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1200000 number of dielectric boundary points 2605 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1047 ## 99 charges are in solution ## iepsmp to db, and charging done at 0.1900000 number of grid points assigned charge 5160 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8076499E-07 2.8569553E-07 midg,1,midg; midg,igrid,midg 2.6537828E-07 4.0443894E-07 1,midg,midg; igrid,midg,midg 4.0346987E-07 2.4577318E-07 gauss-seidel spectral radius is 0.9905851 estimated iterations to convergence 84 setup time was (sec) 0.3100000 now iterating at: 17:03:07 rms-change max change #iterations 0.2046784 32.67457 at 10iterations 2.7390046E-02 4.019403 at 20iterations 3.7188188E-03 0.8112006 at 30iterations 4.9669901E-04 7.7325821E-02 at 40iterations 6.8796537E-05 1.0101318E-02 at 50iterations finished qdiffx linear iterations at : 17:03:09 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 6.8796537E-05 1.0101318E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 17:03:10 3.301u 0.181s 0:03.87 89.9% 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 Mon Oct 10 2011 at 17:03:10 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1361 !!! WARNING: HIT 6 has a net charge of 0.5140 !!! WARNING: HIT 27 has a net charge of 0.5140 !!! WARNING: HIR 47 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.242143 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): 34.63600 82.26900 ymin,ymax (A): 10.92200 52.35900 zmin,zma (A): 25.47000 60.31000 x,y,z range (A): 47.63301 41.43700 34.84000 scale (grids/A): 2.242143 object centre (A): 58.45250 31.64050 42.89000 number of atom coordinates read : 1361 total number of charged atoms : 1238 net assigned charge : 16.04199 assigned positive charge : 213.3342 centred at (gu) : 91.00049 90.98347 85.89831 assigned negative charge : -197.2922 centred at (gu) : 91.40668 90.77642 85.76144 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 51000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12008 grid for indexing accessible points = 1.400000 m= 19117 mr = 33779 m= 4152 mr = 13976 m= 509 mr = 2737 m= 29 mr = 287 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 24016 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 46 iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 9869 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) : 0.7473809 object centre at (A) : 58.45250 31.64050 42.89000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3195491E-02 2.9976388E-02 midg,1,midg; midg,igrid,midg 3.0919304E-02 8.9835808E-02 1,midg,midg; igrid,midg,midg 0.1328012 0.1015109 gauss-seidel spectral radius is 0.9988627 estimated iterations to convergence 235 setup time was (sec) 0.4900000 now iterating at: 17:03:11 rms-change max change #iterations 4.000829 186.8325 at 10iterations 1.991222 78.85384 at 20iterations 0.9948486 36.57922 at 30iterations 0.4960133 18.17425 at 40iterations 0.2467743 8.523107 at 50iterations 0.1242975 4.237043 at 60iterations 6.1919920E-02 2.277571 at 70iterations 3.0877965E-02 1.126425 at 80iterations 1.5414774E-02 0.5459161 at 90iterations 7.6922202E-03 0.2733479 at 100iterations 3.8548131E-03 0.1365051 at 110iterations 1.9209331E-03 6.6717148E-02 at 120iterations finished qdiffx linear iterations at : 17:03:18 total time elapsed so far: 7.410000 # loops : 120 mean,max change (kT/e) : 1.9209331E-03 6.6717148E-02 energy calculations done at 7.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.540000 DelPhi exited at 17:03:19 7.545u 0.200s 0:08.79 88.0% 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 17:03:19 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1361 !!! WARNING: HIT 6 has a net charge of 0.5140 !!! WARNING: HIT 27 has a net charge of 0.5140 !!! WARNING: HIR 47 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.363214 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): 34.63600 82.26900 ymin,ymax (A): 10.92200 52.35900 zmin,zma (A): 25.47000 60.31000 x,y,z range (A): 47.63301 41.43700 34.84000 scale (grids/A): 3.363214 object centre (A): 58.45250 31.64050 42.89000 number of atom coordinates read : 1361 total number of charged atoms : 1238 net assigned charge : 16.04199 assigned positive charge : 213.3342 centred at (gu) : 91.50075 91.47518 83.84762 assigned negative charge : -197.2922 centred at (gu) : 92.11008 91.16463 83.64216 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 117454 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12008 grid for indexing accessible points = 1.400000 m= 58757 mr = 81786 m= 24547 mr = 47443 m= 7889 mr = 19798 m= 1985 mr = 6048 m= 331 mr = 1477 m= 31 mr = 243 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8100000 number of dielectric boundary points 54185 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 9904 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) : 2.242143 object centre at (A) : 58.45250 31.64050 42.89000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3576861 0.1630164 midg,1,midg; midg,igrid,midg 0.1626925 0.7429898 1,midg,midg; igrid,midg,midg 1.037500 0.8054518 gauss-seidel spectral radius is 0.9992981 estimated iterations to convergence 298 setup time was (sec) 1.040000 now iterating at: 17:03:20 rms-change max change #iterations 8.773847 370.0294 at 10iterations 5.135363 118.6037 at 20iterations 2.998213 63.83794 at 30iterations 1.752187 40.88023 at 40iterations 1.019907 21.12317 at 50iterations 0.5942568 11.30491 at 60iterations 0.3461756 7.017005 at 70iterations 0.2009497 4.370543 at 80iterations 0.1171595 2.475365 at 90iterations 6.8131633E-02 1.476502 at 100iterations 3.9620470E-02 0.8167574 at 110iterations 2.3058675E-02 0.4439697 at 120iterations 1.3402450E-02 0.2904747 at 130iterations 7.8288782E-03 0.1487694 at 140iterations 4.5487545E-03 9.6576691E-02 at 150iterations 2.6407950E-03 5.3775787E-02 at 160iterations 1.5378427E-03 2.9373169E-02 at 170iterations 8.9552585E-04 1.9264221E-02 at 180iterations finished qdiffx linear iterations at : 17:03:31 total time elapsed so far: 11.99000 # loops : 180 mean,max change (kT/e) : 8.9552585E-04 1.9264221E-02 energy calculations done at 11.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.12000 DelPhi exited at 17:03:32 12.126u 0.200s 0:13.11 93.9% 0+0k 0+0io 0pf+0w