Sun Oct 9 08:16:57 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 08:16:58 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 = 5066 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5283624 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): -32.57600 25.26300 ymin,ymax (A): -12.72400 54.65400 zmin,zma (A): -29.01100 35.97700 x,y,z range (A): 57.83900 67.37800 64.98800 scale (grids/A): 0.5283624 object centre (A): -3.656500 20.96500 3.483001 number of atom coordinates read : 5066 total number of charged atoms : 4903 net assigned charge : -4.999997 assigned positive charge : 756.9534 centred at (gu) : 88.13301 89.70490 89.69492 assigned negative charge : -761.9594 centred at (gu) : 88.10191 89.56079 89.78488 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 9169 nv = 96 ne = 84 npr = 100945 no. pairs analyzed = 100945 no. exposed pairs = 6634 no. arc points = 45688 no. surface atoms = 2215 nbur = 2851 mkacc time = 0.2400000 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 = 1.624000 m= 365 mr = 4702 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 4819 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4530 ## 606 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 12141 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9441217E-10 -6.1871919E-10 midg,1,midg; midg,igrid,midg -1.0678101E-09 6.1593308E-10 1,midg,midg; igrid,midg,midg -5.2638688E-10 1.7276259E-11 gauss-seidel spectral radius is 0.9817032 estimated iterations to convergence 61 setup time was (sec) 0.7400000 now iterating at: 08:16:58 rms-change max change #iterations 8.3452776E-02 12.17624 at 10iterations 5.3461208E-03 0.7239761 at 20iterations 5.8168685E-04 0.1108589 at 30iterations 1.5639866E-04 3.2821655E-02 at 40iterations 5.2054176E-05 1.0442734E-02 at 50iterations finished qdiffx linear iterations at : 08:17:01 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 5.2054176E-05 1.0442734E-02 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 08:17:02 3.609u 0.150s 0:04.03 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 08:17:02 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 = 5066 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.585087 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): -32.57600 25.26300 ymin,ymax (A): -12.72400 54.65400 zmin,zma (A): -29.01100 35.97700 x,y,z range (A): 57.83900 67.37800 64.98800 scale (grids/A): 1.585087 object centre (A): -3.656500 20.96500 3.483001 number of atom coordinates read : 5066 total number of charged atoms : 4903 net assigned charge : -4.999997 assigned positive charge : 756.9534 centred at (gu) : 84.39737 89.11306 89.08260 assigned negative charge : -761.9594 centred at (gu) : 84.30524 88.68179 89.35428 start vw surface at 0.2300000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 102835 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45688 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 31106 mr = 70255 m= 2870 mr = 20549 m= 66 mr = 1151 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 254 time to turn everything in is 0.7700000 number of dielectric boundary points 44922 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 544 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 37209 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) : 0.5283624 object centre at (A) : -3.656500 20.96500 3.483001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.1884743E-03 -6.6947960E-03 midg,1,midg; midg,igrid,midg -1.6759681E-02 1.1701901E-02 1,midg,midg; igrid,midg,midg -1.8144822E-03 -3.4394874E-03 gauss-seidel spectral radius is 0.9982886 estimated iterations to convergence 192 setup time was (sec) 1.090000 now iterating at: 08:17:03 rms-change max change #iterations 4.250158 180.4271 at 10iterations 1.811909 56.98266 at 20iterations 0.7747392 24.32138 at 30iterations 0.3315532 9.597692 at 40iterations 0.1416745 4.085754 at 50iterations 6.0789123E-02 1.773620 at 60iterations 2.6069701E-02 0.8094730 at 70iterations 1.1209167E-02 0.3153725 at 80iterations 4.8419964E-03 0.1579247 at 90iterations 2.1126030E-03 6.1523438E-02 at 100iterations 9.4989344E-04 3.0029297E-02 at 110iterations 4.4790935E-04 1.5127420E-02 at 120iterations finished qdiffx linear iterations at : 08:17:10 total time elapsed so far: 8.290000 # loops : 120 mean,max change (kT/e) : 4.4790935E-04 1.5127420E-02 energy calculations done at 8.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.480000 DelPhi exited at 08:17:11 8.487u 0.213s 0:08.98 96.7% 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 08:17:11 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 = 5066 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.377631 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): -32.57600 25.26300 ymin,ymax (A): -12.72400 54.65400 zmin,zma (A): -29.01100 35.97700 x,y,z range (A): 57.83900 67.37800 64.98800 scale (grids/A): 2.377631 object centre (A): -3.656500 20.96500 3.483001 number of atom coordinates read : 5066 total number of charged atoms : 4903 net assigned charge : -4.999997 assigned positive charge : 756.9534 centred at (gu) : 81.59573 88.66885 88.62331 assigned negative charge : -761.9594 centred at (gu) : 81.45789 88.02269 89.03147 start vw surface at 0.2200000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 238989 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45688 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 109988 mr = 172574 m= 29081 mr = 85352 m= 4092 mr = 20753 m= 232 mr = 2378 m= 1 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 1.130000 no. cavity mid-points inaccessible to solvent = 881 time to turn everything in is 1.890000 number of dielectric boundary points 101255 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 54 iepsmp to db, and charging done at 2.050000 number of grid points assigned charge 39147 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) : 1.585087 object centre at (A) : -3.656500 20.96500 3.483001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1743863 3.6170524E-02 midg,1,midg; midg,igrid,midg -0.2294473 0.1464313 1,midg,midg; igrid,midg,midg 5.6676723E-02 -7.6653078E-02 gauss-seidel spectral radius is 0.9992325 estimated iterations to convergence 285 setup time was (sec) 2.240000 now iterating at: 08:17:13 rms-change max change #iterations 11.35331 255.5346 at 10iterations 6.738305 139.2751 at 20iterations 3.955117 97.19292 at 30iterations 2.316389 47.54155 at 40iterations 1.348372 27.84547 at 50iterations 0.7805203 14.72850 at 60iterations 0.4513891 8.238871 at 70iterations 0.2601229 4.466001 at 80iterations 0.1495410 2.568516 at 90iterations 8.5920677E-02 1.434045 at 100iterations 4.9216326E-02 0.8075428 at 110iterations 2.8248603E-02 0.5203896 at 120iterations 1.6226996E-02 0.2958584 at 130iterations 9.2957402E-03 0.1621780 at 140iterations 5.3368486E-03 8.9744568E-02 at 150iterations 3.0783904E-03 5.4807305E-02 at 160iterations 1.7867334E-03 3.0529022E-02 at 170iterations 1.0487626E-03 1.8386841E-02 at 180iterations finished qdiffx linear iterations at : 08:17:25 total time elapsed so far: 14.13000 # loops : 180 mean,max change (kT/e) : 1.0487626E-03 1.8386841E-02 energy calculations done at 14.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.33000 DelPhi exited at 08:17:26 14.334u 0.226s 0:14.88 97.7% 0+0k 0+0io 0pf+0w