Tue Oct 11 04:30:02 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 Tue Oct 11 2011 at 04:30:02 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6508226 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): -12.32700 36.98200 ymin,ymax (A): -25.81400 22.63800 zmin,zma (A): -9.498000 45.20200 x,y,z range (A): 49.30900 48.45200 54.70000 scale (grids/A): 0.6508226 object centre (A): 12.32750 -1.587999 17.85200 number of atom coordinates read : 2750 total number of charged atoms : 2598 net assigned charge : 2.162012 assigned positive charge : 413.4607 centred at (gu) : 90.41369 90.48788 91.68185 assigned negative charge : -411.2993 centred at (gu) : 90.15714 90.29829 91.58272 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7725 nv = 96 ne = 84 npr = 56916 no. pairs analyzed = 56916 no. exposed pairs = 3294 no. arc points = 22710 no. surface atoms = 1111 nbur = 1639 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 387 mr = 4416 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.2000000 number of dielectric boundary points 3662 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2276 ## 226 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 9287 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.9059640E-09 2.8482740E-08 midg,1,midg; midg,igrid,midg -2.5379133E-08 3.8079026E-08 1,midg,midg; igrid,midg,midg -3.6379429E-08 4.8972741E-08 gauss-seidel spectral radius is 0.9877736 estimated iterations to convergence 74 setup time was (sec) 0.3900000 now iterating at: 04:30:03 rms-change max change #iterations 0.1609805 21.12281 at 10iterations 1.6979948E-02 2.241744 at 20iterations 1.8053398E-03 0.2495308 at 30iterations 2.0332968E-04 2.8228760E-02 at 40iterations 3.0310017E-05 3.5057068E-03 at 50iterations finished qdiffx linear iterations at : 04:30:06 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 3.0310017E-05 3.5057068E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 04:30:06 3.379u 0.174s 0:04.18 84.6% 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 04:30:06 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.952468 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): -12.32700 36.98200 ymin,ymax (A): -25.81400 22.63800 zmin,zma (A): -9.498000 45.20200 x,y,z range (A): 49.30900 48.45200 54.70000 scale (grids/A): 1.952468 object centre (A): 12.32750 -1.587999 17.85200 number of atom coordinates read : 2750 total number of charged atoms : 2598 net assigned charge : 2.162012 assigned positive charge : 413.4607 centred at (gu) : 91.24037 91.46299 95.04495 assigned negative charge : -411.2993 centred at (gu) : 90.47140 90.89477 94.74783 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 83103 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22710 grid for indexing accessible points = 1.400000 m= 30635 mr = 58927 m= 4860 mr = 23059 m= 306 mr = 3208 m= 3 mr = 102 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1190 time to turn everything in is 0.4000000 number of dielectric boundary points 33611 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 157 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 20494 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) : 0.6508226 object centre at (A) : 12.32750 -1.587999 17.85200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.3701168E-02 7.0112958E-03 midg,1,midg; midg,igrid,midg -1.5439662E-02 3.1174693E-02 1,midg,midg; igrid,midg,midg -8.8293068E-03 6.5044411E-02 gauss-seidel spectral radius is 0.9987083 estimated iterations to convergence 220 setup time was (sec) 0.6200000 now iterating at: 04:30:07 rms-change max change #iterations 4.558678 190.5828 at 10iterations 2.189636 74.91737 at 20iterations 1.048761 33.15393 at 30iterations 0.5030403 14.48160 at 40iterations 0.2404260 7.290966 at 50iterations 0.1158200 3.150372 at 60iterations 5.5336144E-02 1.764894 at 70iterations 2.6500426E-02 0.7788162 at 80iterations 1.2708366E-02 0.4184418 at 90iterations 6.0921847E-03 0.1807442 at 100iterations 2.9120820E-03 8.9332581E-02 at 110iterations 1.3961057E-03 3.9379418E-02 at 120iterations finished qdiffx linear iterations at : 04:30:14 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 1.3961057E-03 3.9379418E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 04:30:15 7.819u 0.207s 0:08.58 93.3% 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 04:30:15 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.928702 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): -12.32700 36.98200 ymin,ymax (A): -25.81400 22.63800 zmin,zma (A): -9.498000 45.20200 x,y,z range (A): 49.30900 48.45200 54.70000 scale (grids/A): 2.928702 object centre (A): 12.32750 -1.587999 17.85200 number of atom coordinates read : 2750 total number of charged atoms : 2598 net assigned charge : 2.162012 assigned positive charge : 413.4607 centred at (gu) : 91.86040 92.19440 97.56718 assigned negative charge : -411.2993 centred at (gu) : 90.70689 91.34206 97.12164 start vw surface at 0.1000000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 192264 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22710 grid for indexing accessible points = 1.400000 m= 99225 mr = 142387 m= 36201 mr = 82481 m= 8844 mr = 29642 m= 1239 mr = 6782 m= 72 mr = 845 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 4054 time to turn everything in is 1.070000 number of dielectric boundary points 75684 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 20777 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) : 1.952468 object centre at (A) : 12.32750 -1.587999 17.85200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.019328 0.2547522 midg,1,midg; midg,igrid,midg -0.1717130 0.3516878 1,midg,midg; igrid,midg,midg -1.7745327E-02 0.5106838 gauss-seidel spectral radius is 0.9992743 estimated iterations to convergence 293 setup time was (sec) 1.310000 now iterating at: 04:30:16 rms-change max change #iterations 10.59203 421.7590 at 10iterations 6.199474 118.3544 at 20iterations 3.618439 69.60896 at 30iterations 2.114203 41.50351 at 40iterations 1.228219 22.31550 at 50iterations 0.7154263 13.21009 at 60iterations 0.4153045 8.057890 at 70iterations 0.2415168 4.376698 at 80iterations 0.1401701 2.519176 at 90iterations 8.1215940E-02 1.437546 at 100iterations 4.7058858E-02 0.7912445 at 110iterations 2.7286010E-02 0.4671955 at 120iterations 1.5857214E-02 0.3051682 at 130iterations 9.2047295E-03 0.1533966 at 140iterations 5.3437743E-03 0.1019821 at 150iterations 3.1168414E-03 5.1313400E-02 at 160iterations 1.8349689E-03 3.6186218E-02 at 170iterations 1.0888426E-03 1.8595845E-02 at 180iterations finished qdiffx linear iterations at : 04:30:28 total time elapsed so far: 12.71000 # loops : 180 mean,max change (kT/e) : 1.0888426E-03 1.8595845E-02 energy calculations done at 12.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.85000 DelPhi exited at 04:30:28 12.850u 0.203s 0:13.46 96.9% 0+0k 0+0io 0pf+0w