Tue Oct 11 03:20:41 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 Tue Oct 11 2011 at 03:20:42 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3212 !!! WARNING: GLM 12 has a net charge of -0.0940 !!! WARNING: SEP 223 has a net charge of -0.4750 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: 0.5363547 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): 60.00800 110.1740 ymin,ymax (A): -3.163000 56.11200 zmin,zma (A): 36.03600 102.4100 x,y,z range (A): 50.16600 59.27500 66.37399 scale (grids/A): 0.5363547 object centre (A): 85.09100 26.47450 69.22300 number of atom coordinates read : 3212 total number of charged atoms : 3067 net assigned charge : -6.568974 assigned positive charge : 482.6008 centred at (gu) : 88.93948 91.57957 92.80922 assigned negative charge : -489.1708 centred at (gu) : 88.97697 91.56577 92.83616 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5822 nv = 96 ne = 84 npr = 66660 no. pairs analyzed = 66660 no. exposed pairs = 3968 no. arc points = 27356 no. surface atoms = 1340 nbur = 1872 mkacc time = 0.1900000 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 = 1.596000 m= 229 mr = 3055 m= 0 mr = 7 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 2989 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2807 ## 405 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 7775 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.3373668E-11 -8.3022966E-10 midg,1,midg; midg,igrid,midg -2.3312030E-10 -3.0070510E-10 1,midg,midg; igrid,midg,midg -1.1060391E-10 -3.5531128E-10 gauss-seidel spectral radius is 0.9820976 estimated iterations to convergence 62 setup time was (sec) 0.6900000 now iterating at: 03:20:42 rms-change max change #iterations 7.1678683E-02 13.43967 at 10iterations 4.6561067E-03 0.7868462 at 20iterations 4.0468600E-04 6.6985607E-02 at 30iterations 6.1197155E-05 1.2258053E-02 at 40iterations 1.2584678E-05 2.6242733E-03 at 50iterations finished qdiffx linear iterations at : 03:20:46 total time elapsed so far: 4.130000 # loops : 50 mean,max change (kT/e) : 1.2584678E-05 2.6242733E-03 energy calculations done at 4.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.320000 DelPhi exited at 03:20:46 4.320u 0.291s 0:04.91 93.8% 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 03:20:46 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3212 !!! WARNING: GLM 12 has a net charge of -0.0940 !!! WARNING: SEP 223 has a net charge of -0.4750 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: 1.609064 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): 60.00800 110.1740 ymin,ymax (A): -3.163000 56.11200 zmin,zma (A): 36.03600 102.4100 x,y,z range (A): 50.16600 59.27500 66.37399 scale (grids/A): 1.609064 object centre (A): 85.09100 26.47450 69.22300 number of atom coordinates read : 3212 total number of charged atoms : 3067 net assigned charge : -6.568974 assigned positive charge : 482.6008 centred at (gu) : 86.81776 94.73780 98.42650 assigned negative charge : -489.1708 centred at (gu) : 86.93085 94.69663 98.50812 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 64528 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27356 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 19405 mr = 43732 m= 1986 mr = 13441 m= 45 mr = 963 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 294 time to turn everything in is 0.6000000 number of dielectric boundary points 27828 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 358 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 23376 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) : 0.5363547 object centre at (A) : 85.09100 26.47450 69.22300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4413884E-02 -1.5159629E-02 midg,1,midg; midg,igrid,midg -3.7439931E-03 4.0358864E-03 1,midg,midg; igrid,midg,midg -3.9443355E-03 -6.0087955E-03 gauss-seidel spectral radius is 0.9981372 estimated iterations to convergence 184 setup time was (sec) 0.9100000 now iterating at: 03:20:48 rms-change max change #iterations 3.380140 151.4365 at 10iterations 1.387130 48.00718 at 20iterations 0.5712494 20.69286 at 30iterations 0.2356455 8.710432 at 40iterations 9.7638994E-02 3.579514 at 50iterations 4.0235821E-02 1.460579 at 60iterations 1.6625270E-02 0.6216736 at 70iterations 6.8699187E-03 0.2668095 at 80iterations 2.8582637E-03 0.1062889 at 90iterations 1.1951339E-03 4.5753479E-02 at 100iterations 5.0424086E-04 1.7682076E-02 at 110iterations 2.1932976E-04 8.0103874E-03 at 120iterations finished qdiffx linear iterations at : 03:20:56 total time elapsed so far: 9.560000 # loops : 120 mean,max change (kT/e) : 2.1932976E-04 8.0103874E-03 energy calculations done at 9.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.740000 DelPhi exited at 03:20:57 9.738u 0.345s 0:10.74 93.7% 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 Tue Oct 11 2011 at 03:20:57 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3212 !!! WARNING: GLM 12 has a net charge of -0.0940 !!! WARNING: SEP 223 has a net charge of -0.4750 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: 2.413596 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): 60.00800 110.1740 ymin,ymax (A): -3.163000 56.11200 zmin,zma (A): 36.03600 102.4100 x,y,z range (A): 50.16600 59.27500 66.37399 scale (grids/A): 2.413596 object centre (A): 85.09100 26.47450 69.22300 number of atom coordinates read : 3212 total number of charged atoms : 3067 net assigned charge : -6.568974 assigned positive charge : 482.6008 centred at (gu) : 85.22650 97.10648 102.6395 assigned negative charge : -489.1708 centred at (gu) : 85.39603 97.04481 102.7622 start vw surface at 0.1800000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 150075 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27356 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 68139 mr = 107202 m= 18682 mr = 53870 m= 2990 mr = 14105 m= 187 mr = 1945 m= 2 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.8299999 no. cavity mid-points inaccessible to solvent = 1096 time to turn everything in is 1.460000 number of dielectric boundary points 62872 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 24502 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) : 1.609064 object centre at (A) : 85.09100 26.47450 69.22300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4348234 -0.3791118 midg,1,midg; midg,igrid,midg 9.8484789E-04 0.1757079 1,midg,midg; igrid,midg,midg -5.2004542E-02 -8.2811028E-02 gauss-seidel spectral radius is 0.9991242 estimated iterations to convergence 267 setup time was (sec) 1.810000 now iterating at: 03:20:59 rms-change max change #iterations 8.828965 292.3907 at 10iterations 4.941493 130.3444 at 20iterations 2.741665 63.14925 at 30iterations 1.515356 37.38932 at 40iterations 0.8351895 18.00200 at 50iterations 0.4598545 10.58900 at 60iterations 0.2525212 5.704504 at 70iterations 0.1384863 2.893976 at 80iterations 7.5942896E-02 1.550026 at 90iterations 4.1702732E-02 0.8628731 at 100iterations 2.2790827E-02 0.4986864 at 110iterations 1.2516856E-02 0.2444525 at 120iterations 6.8577467E-03 0.1583710 at 130iterations 3.7634668E-03 8.4948540E-02 at 140iterations 2.0722041E-03 4.3604851E-02 at 150iterations 1.1453853E-03 2.4014473E-02 at 160iterations 6.4147508E-04 1.3658285E-02 at 170iterations 3.6380254E-04 7.5364113E-03 at 180iterations finished qdiffx linear iterations at : 03:21:14 total time elapsed so far: 16.07000 # loops : 180 mean,max change (kT/e) : 3.6380254E-04 7.5364113E-03 energy calculations done at 16.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.26000 DelPhi exited at 03:21:14 16.259u 0.328s 0:16.92 97.9% 0+0k 0+0io 0pf+0w