Sun Oct 9 10:29:47 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 Sun Oct 9 2011 at 10:29:47 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2146 !!! WARNING: HIR 524 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6543877 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): -1.296000 48.78600 ymin,ymax (A): -27.55300 26.40200 zmin,zma (A): -5.925000 48.47700 x,y,z range (A): 50.08200 53.95500 54.40200 scale (grids/A): 0.6543877 object centre (A): 23.74500 -0.5754995 21.27600 number of atom coordinates read : 2146 total number of charged atoms : 2009 net assigned charge : -0.4859855 assigned positive charge : 310.7946 centred at (gu) : 90.36069 92.62606 91.18778 assigned negative charge : -311.2814 centred at (gu) : 90.41044 92.44955 91.16764 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6392 nv = 96 ne = 84 npr = 42761 no. pairs analyzed = 42761 no. exposed pairs = 2917 no. arc points = 20664 no. surface atoms = 986 nbur = 1160 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 381 mr = 3313 m= 0 mr = 57 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3403 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1956 ## 158 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7302 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.5013406E-09 1.3011692E-09 midg,1,midg; midg,igrid,midg -1.5100692E-08 3.8699234E-08 1,midg,midg; igrid,midg,midg 4.6178581E-09 -9.2347214E-09 gauss-seidel spectral radius is 0.9878691 estimated iterations to convergence 74 setup time was (sec) 0.3600000 now iterating at: 10:29:48 rms-change max change #iterations 0.1393367 25.61973 at 10iterations 1.4786453E-02 2.358612 at 20iterations 1.5086372E-03 0.2280617 at 30iterations 1.5861217E-04 3.0107021E-02 at 40iterations 1.6497883E-05 2.4623871E-03 at 50iterations finished qdiffx linear iterations at : 10:29:50 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 1.6497883E-05 2.4623871E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 10:29:51 3.338u 0.173s 0:03.85 90.9% 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 Sun Oct 9 2011 at 10:29:51 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2146 !!! WARNING: HIR 524 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.963163 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): -1.296000 48.78600 ymin,ymax (A): -27.55300 26.40200 zmin,zma (A): -5.925000 48.47700 x,y,z range (A): 50.08200 53.95500 54.40200 scale (grids/A): 1.963163 object centre (A): 23.74500 -0.5754995 21.27600 number of atom coordinates read : 2146 total number of charged atoms : 2009 net assigned charge : -0.4859855 assigned positive charge : 310.7946 centred at (gu) : 91.08174 97.87797 93.56332 assigned negative charge : -311.2814 centred at (gu) : 91.23168 97.34894 93.50294 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 68083 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20664 grid for indexing accessible points = 1.400000 m= 24233 mr = 44875 m= 4211 mr = 17555 m= 342 mr = 2740 m= 8 mr = 162 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 866 time to turn everything in is 0.3500000 number of dielectric boundary points 31545 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 103 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 15889 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) : 0.6543877 object centre at (A) : 23.74500 -0.5754995 21.27600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0879586E-02 3.9538682E-02 midg,1,midg; midg,igrid,midg -7.5549493E-03 5.1735997E-02 1,midg,midg; igrid,midg,midg -2.0176010E-02 -3.3821657E-02 gauss-seidel spectral radius is 0.9986763 estimated iterations to convergence 218 setup time was (sec) 0.5700000 now iterating at: 10:29:52 rms-change max change #iterations 4.018567 181.6111 at 10iterations 1.897556 69.81519 at 20iterations 0.9005152 29.49520 at 30iterations 0.4290890 14.57144 at 40iterations 0.2026867 6.823011 at 50iterations 9.6168272E-02 3.652292 at 60iterations 4.5681737E-02 1.465027 at 70iterations 2.1553839E-02 0.7032318 at 80iterations 1.0229575E-02 0.3631210 at 90iterations 4.8602005E-03 0.1596756 at 100iterations 2.2969432E-03 7.6511383E-02 at 110iterations 1.0901835E-03 3.3922195E-02 at 120iterations finished qdiffx linear iterations at : 10:29:59 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 1.0901835E-03 3.3922195E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 10:29:59 7.776u 0.196s 0:08.28 96.1% 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 10:29:59 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2146 !!! WARNING: HIR 524 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.944745 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): -1.296000 48.78600 ymin,ymax (A): -27.55300 26.40200 zmin,zma (A): -5.925000 48.47700 x,y,z range (A): 50.08200 53.95500 54.40200 scale (grids/A): 2.944745 object centre (A): 23.74500 -0.5754995 21.27600 number of atom coordinates read : 2146 total number of charged atoms : 2009 net assigned charge : -0.4859855 assigned positive charge : 310.7946 centred at (gu) : 91.62254 101.8169 95.34502 assigned negative charge : -311.2814 centred at (gu) : 91.84763 101.0234 95.25440 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 156931 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20664 grid for indexing accessible points = 1.400000 m= 76736 mr = 109020 m= 29447 mr = 61699 m= 7904 mr = 23615 m= 1359 mr = 6066 m= 109 mr = 960 m= 0 mr = 53 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 2952 time to turn everything in is 0.9200000 number of dielectric boundary points 71073 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 16072 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) : 1.963163 object centre at (A) : 23.74500 -0.5754995 21.27600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6078594E-02 0.5142568 midg,1,midg; midg,igrid,midg -8.7598331E-02 0.3825735 1,midg,midg; igrid,midg,midg -0.2524293 -0.3657501 gauss-seidel spectral radius is 0.9992731 estimated iterations to convergence 293 setup time was (sec) 1.150000 now iterating at: 10:30:01 rms-change max change #iterations 9.303461 575.6802 at 10iterations 5.407135 121.4056 at 20iterations 3.136782 61.92702 at 30iterations 1.818169 35.48548 at 40iterations 1.052251 20.77654 at 50iterations 0.6090079 13.13176 at 60iterations 0.3516200 6.620571 at 70iterations 0.2028079 3.881908 at 80iterations 0.1172922 2.212309 at 90iterations 6.7575783E-02 1.376821 at 100iterations 3.9066479E-02 0.7338696 at 110iterations 2.2524042E-02 0.5045085 at 120iterations 1.3003269E-02 0.2415168 at 130iterations 7.5156111E-03 0.1378174 at 140iterations 4.3328577E-03 7.9299927E-02 at 150iterations 2.4985939E-03 4.3033600E-02 at 160iterations 1.4434161E-03 2.7042866E-02 at 170iterations 8.3352241E-04 1.5861988E-02 at 180iterations finished qdiffx linear iterations at : 10:30:12 total time elapsed so far: 12.51000 # loops : 180 mean,max change (kT/e) : 8.3352241E-04 1.5861988E-02 energy calculations done at 12.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.64000 DelPhi exited at 10:30:13 12.647u 0.212s 0:13.25 96.9% 0+0k 0+0io 0pf+0w