Sat Oct 8 17:34:03 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 Sat Oct 8 2011 at 17:34:03 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 = 3530 !!! WARNING: ILE 447 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5243854 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): -2.462000 45.05800 ymin,ymax (A): -30.37100 26.26100 zmin,zma (A): 1.335000 69.22400 x,y,z range (A): 47.52000 56.63200 67.88900 scale (grids/A): 0.5243854 object centre (A): 21.29800 -2.055000 35.27950 number of atom coordinates read : 3530 total number of charged atoms : 3383 net assigned charge : -5.271986 assigned positive charge : 535.1331 centred at (gu) : 90.80373 91.80693 90.58697 assigned negative charge : -540.4067 centred at (gu) : 90.77085 91.75934 90.57578 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6123 nv = 96 ne = 84 npr = 72732 no. pairs analyzed = 72732 no. exposed pairs = 4296 no. arc points = 29267 no. surface atoms = 1466 nbur = 2064 mkacc time = 0.1600000 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= 214 mr = 3211 m= 2 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3121 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3028 ## 449 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8180 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5445110E-10 -1.1721757E-10 midg,1,midg; midg,igrid,midg -1.9376477E-10 4.3100416E-11 1,midg,midg; igrid,midg,midg -2.0770252E-10 -3.1295407E-11 gauss-seidel spectral radius is 0.9813007 estimated iterations to convergence 60 setup time was (sec) 0.5700000 now iterating at: 17:34:04 rms-change max change #iterations 6.6178553E-02 10.38777 at 10iterations 4.0844227E-03 0.6895218 at 20iterations 4.3942349E-04 8.5284233E-02 at 30iterations 1.1029711E-04 2.3741722E-02 at 40iterations 3.1471543E-05 6.6814423E-03 at 50iterations finished qdiffx linear iterations at : 17:34:07 total time elapsed so far: 3.030000 # loops : 50 mean,max change (kT/e) : 3.1471543E-05 6.6814423E-03 energy calculations done at 3.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.200000 DelPhi exited at 17:34:07 3.207u 0.134s 0:03.65 91.2% 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 Sat Oct 8 2011 at 17:34:07 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 = 3530 !!! WARNING: ILE 447 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.573156 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): -2.462000 45.05800 ymin,ymax (A): -30.37100 26.26100 zmin,zma (A): 1.335000 69.22400 x,y,z range (A): 47.52000 56.63200 67.88900 scale (grids/A): 1.573156 object centre (A): 21.29800 -2.055000 35.27950 number of atom coordinates read : 3530 total number of charged atoms : 3383 net assigned charge : -5.271986 assigned positive charge : 535.1331 centred at (gu) : 92.41016 95.41972 91.75986 assigned negative charge : -540.4067 centred at (gu) : 92.31218 95.27760 91.72679 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 68514 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29267 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 20467 mr = 47361 m= 1918 mr = 13966 m= 37 mr = 856 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 692 time to turn everything in is 0.4700000 number of dielectric boundary points 28753 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 388 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 25639 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) : 0.5243854 object centre at (A) : 21.29800 -2.055000 35.27950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6502138E-03 8.5644554E-03 midg,1,midg; midg,igrid,midg -7.2540399E-03 -1.0470085E-02 1,midg,midg; igrid,midg,midg -2.3251541E-03 4.0516211E-04 gauss-seidel spectral radius is 0.9980795 estimated iterations to convergence 181 setup time was (sec) 0.7400000 now iterating at: 17:34:08 rms-change max change #iterations 3.368397 142.6372 at 10iterations 1.366673 50.18194 at 20iterations 0.5566696 18.60004 at 30iterations 0.2274127 9.155542 at 40iterations 9.2488393E-02 3.234764 at 50iterations 3.7660513E-02 1.332645 at 60iterations 1.5404657E-02 0.5599067 at 70iterations 6.2775062E-03 0.2171631 at 80iterations 2.6031989E-03 9.8226547E-02 at 90iterations 1.0940972E-03 3.8305521E-02 at 100iterations 4.7918863E-04 1.7783642E-02 at 110iterations 2.2625785E-04 9.4184875E-03 at 120iterations finished qdiffx linear iterations at : 17:34:14 total time elapsed so far: 6.770000 # loops : 120 mean,max change (kT/e) : 2.2625785E-04 9.4184875E-03 energy calculations done at 6.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.940000 DelPhi exited at 17:34:15 6.947u 0.153s 0:07.42 95.5% 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 Sat Oct 8 2011 at 17:34:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3530 !!! WARNING: ILE 447 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.359734 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): -2.462000 45.05800 ymin,ymax (A): -30.37100 26.26100 zmin,zma (A): 1.335000 69.22400 x,y,z range (A): 47.52000 56.63200 67.88900 scale (grids/A): 2.359734 object centre (A): 21.29800 -2.055000 35.27950 number of atom coordinates read : 3530 total number of charged atoms : 3383 net assigned charge : -5.271986 assigned positive charge : 535.1331 centred at (gu) : 93.61516 98.12946 92.63956 assigned negative charge : -540.4067 centred at (gu) : 93.46807 97.91625 92.59016 start vw surface at 0.1600000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 159582 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29267 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 72461 mr = 116136 m= 19202 mr = 57363 m= 2766 mr = 14173 m= 168 mr = 1738 m= 1 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 2431 time to turn everything in is 1.120000 number of dielectric boundary points 64720 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 45 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 27010 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) : 1.573156 object centre at (A) : 21.29800 -2.055000 35.27950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2625819 2.7037254E-02 midg,1,midg; midg,igrid,midg -0.1058500 -0.1569629 1,midg,midg; igrid,midg,midg -3.9651621E-02 4.1633222E-02 gauss-seidel spectral radius is 0.9991105 estimated iterations to convergence 265 setup time was (sec) 1.400000 now iterating at: 17:34:16 rms-change max change #iterations 8.914490 280.0051 at 10iterations 4.946331 123.5050 at 20iterations 2.736695 72.33860 at 30iterations 1.499320 31.30927 at 40iterations 0.8250065 18.04410 at 50iterations 0.4497514 9.389099 at 60iterations 0.2465847 5.634968 at 70iterations 0.1344874 3.050048 at 80iterations 7.3332854E-02 1.430263 at 90iterations 3.9898872E-02 0.8330803 at 100iterations 2.1793306E-02 0.4733806 at 110iterations 1.1879827E-02 0.2590332 at 120iterations 6.4919223E-03 0.1325760 at 130iterations 3.5424747E-03 7.0896149E-02 at 140iterations 1.9422467E-03 4.1320801E-02 at 150iterations 1.0689540E-03 2.2540092E-02 at 160iterations 5.9413596E-04 1.1880398E-02 at 170iterations 3.3571731E-04 6.7137480E-03 at 180iterations finished qdiffx linear iterations at : 17:34:26 total time elapsed so far: 10.89000 # loops : 180 mean,max change (kT/e) : 3.3571731E-04 6.7137480E-03 energy calculations done at 10.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.06000 DelPhi exited at 17:34:26 11.063u 0.173s 0:11.54 97.3% 0+0k 0+0io 0pf+0w