Thu Jan 19 13:34:41 PST 2012 #!/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 Thu Jan 19 2012 at 13:34:43 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: 330 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 7386 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.4527937 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): -4.137000 73.45900 ymin,ymax (A): -11.79400 66.82900 zmin,zma (A): 6.993001 74.76200 x,y,z range (A): 77.59600 78.62300 67.76900 scale (grids/A): 0.4527937 object centre (A): 34.66100 27.51750 40.87750 number of atom coordinates read : 7386 total number of charged atoms : 7210 net assigned charge : 4.000047 assigned positive charge : 1135.009 centred at (gu) : 90.49640 90.23395 90.13432 assigned negative charge : -1131.017 centred at (gu) : 90.39703 90.30097 90.07106 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8896 nv = 96 ne = 84 npr = 149414 no. pairs analyzed = 149414 no. exposed pairs = 9669 no. arc points = 65132 no. surface atoms = 3247 nbur = 4139 mkacc time = 0.2500000 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 = 1.904000 m= 253 mr = 4158 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 4991 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5843 ## 1120 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 12478 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2647089E-11 1.9679354E-11 midg,1,midg; midg,igrid,midg 1.8516416E-11 -1.5180034E-11 1,midg,midg; igrid,midg,midg -1.9434452E-11 3.2292294E-11 gauss-seidel spectral radius is 0.9752654 estimated iterations to convergence 53 setup time was (sec) 0.6700000 now iterating at: 13:34:47 rms-change max change #iterations 4.2150673E-02 7.170059 at 10iterations 2.0612904E-03 0.2972593 at 20iterations 4.4312736E-04 5.5208206E-02 at 30iterations 1.6334478E-04 1.9267559E-02 at 40iterations 6.1724902E-05 7.1382523E-03 at 50iterations finished qdiffx linear iterations at : 13:34:59 total time elapsed so far: 3.840000 # loops : 50 mean,max change (kT/e) : 6.1724902E-05 7.1382523E-03 energy calculations done at 3.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.970000 DelPhi exited at 13:34:59 3.974u 0.219s 0:16.71 25.0% 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 Thu Jan 19 2012 at 13:35:00 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: 330 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 7386 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.358381 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): -4.137000 73.45900 ymin,ymax (A): -11.79400 66.82900 zmin,zma (A): 6.993001 74.76200 x,y,z range (A): 77.59600 78.62300 67.76900 scale (grids/A): 1.358381 object centre (A): 34.66100 27.51750 40.87750 number of atom coordinates read : 7386 total number of charged atoms : 7210 net assigned charge : 4.000047 assigned positive charge : 1135.009 centred at (gu) : 91.48746 90.70103 90.40145 assigned negative charge : -1131.017 centred at (gu) : 91.19089 90.90306 90.21308 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 103789 reading accessible surface arcs data from file ARCDAT no. of arc points read = 65132 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.764000 m= 24141 mr = 68476 m= 1342 mr = 13771 m= 9 mr = 291 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 97 time to turn everything in is 0.5400000 number of dielectric boundary points 46743 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1173 ## 45 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 51454 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) : 0.4527937 object centre at (A) : 34.66100 27.51750 40.87750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6619698E-03 3.9116009E-03 midg,1,midg; midg,igrid,midg 9.7414143E-03 4.0166988E-03 1,midg,midg; igrid,midg,midg -1.6984308E-02 1.4705602E-02 gauss-seidel spectral radius is 0.9977543 estimated iterations to convergence 168 setup time was (sec) 0.7700000 now iterating at: 13:35:01 rms-change max change #iterations 3.687135 154.4407 at 10iterations 1.392156 43.98802 at 20iterations 0.5243221 18.03605 at 30iterations 0.1986550 6.799774 at 40iterations 7.5266540E-02 2.331501 at 50iterations 2.8559608E-02 0.8932829 at 60iterations 1.0910359E-02 0.3980825 at 70iterations 4.2242305E-03 0.1463346 at 80iterations 1.7061456E-03 5.1683426E-02 at 90iterations 7.7202421E-04 2.4781704E-02 at 100iterations 4.0980545E-04 1.2908936E-02 at 110iterations 2.5201423E-04 6.6776276E-03 at 120iterations finished qdiffx linear iterations at : 13:35:19 total time elapsed so far: 8.190000 # loops : 120 mean,max change (kT/e) : 2.5201423E-04 6.6776276E-03 energy calculations done at 8.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.320000 DelPhi exited at 13:35:20 8.322u 0.212s 0:20.12 42.3% 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 Thu Jan 19 2012 at 13:35:20 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: 330 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 7386 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.037572 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): -4.137000 73.45900 ymin,ymax (A): -11.79400 66.82900 zmin,zma (A): 6.993001 74.76200 x,y,z range (A): 77.59600 78.62300 67.76900 scale (grids/A): 2.037572 object centre (A): 34.66100 27.51750 40.87750 number of atom coordinates read : 7386 total number of charged atoms : 7210 net assigned charge : 4.000047 assigned positive charge : 1135.009 centred at (gu) : 92.23100 91.05147 90.60194 assigned negative charge : -1131.017 centred at (gu) : 91.78654 91.35462 90.31942 start vw surface at 0.1800000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 243563 reading accessible surface arcs data from file ARCDAT no. of arc points read = 65132 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.764000 m= 93382 mr = 170761 m= 16700 mr = 67820 m= 1453 mr = 10110 m= 36 mr = 629 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 322 time to turn everything in is 1.250000 number of dielectric boundary points 105815 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 319 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 57135 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) : 1.358381 object centre at (A) : 34.66100 27.51750 40.87750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1035532 9.0977274E-02 midg,1,midg; midg,igrid,midg 0.3498899 1.7073315E-02 1,midg,midg; igrid,midg,midg -0.5802615 0.2268734 gauss-seidel spectral radius is 0.9991064 estimated iterations to convergence 264 setup time was (sec) 1.510000 now iterating at: 13:35:23 rms-change max change #iterations 11.05620 270.1112 at 10iterations 6.254396 140.5827 at 20iterations 3.512904 74.86782 at 30iterations 1.959077 43.22581 at 40iterations 1.087766 24.40441 at 50iterations 0.6004178 12.79826 at 60iterations 0.3305492 7.395288 at 70iterations 0.1820523 3.322896 at 80iterations 0.1000595 2.049604 at 90iterations 5.4824974E-02 1.075714 at 100iterations 3.0007886E-02 0.5601845 at 110iterations 1.6409922E-02 0.3140430 at 120iterations 8.9708054E-03 0.1703053 at 130iterations 4.9091685E-03 9.5779419E-02 at 140iterations 2.6794369E-03 5.1208496E-02 at 150iterations 1.4669423E-03 2.6664734E-02 at 160iterations 8.0509647E-04 1.5170097E-02 at 170iterations 4.4302645E-04 9.2048645E-03 at 180iterations finished qdiffx linear iterations at : 13:35:49 total time elapsed so far: 14.28000 # loops : 180 mean,max change (kT/e) : 4.4302645E-04 9.2048645E-03 energy calculations done at 14.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.41000 DelPhi exited at 13:35:50 14.415u 0.246s 0:29.90 48.9% 0+0k 0+0io 0pf+0w