Tue Oct 11 06:46:29 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 06:46:29 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 = 4190 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: 0.5079836 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): -7.616000 62.46500 ymin,ymax (A): -109.7220 -49.35900 zmin,zma (A): -113.5750 -65.34500 x,y,z range (A): 70.08100 60.36300 48.23000 scale (grids/A): 0.5079836 object centre (A): 27.42450 -79.54050 -89.46001 number of atom coordinates read : 4190 total number of charged atoms : 4043 net assigned charge : -0.4999840 assigned positive charge : 629.2817 centred at (gu) : 89.60073 92.33855 90.36976 assigned negative charge : -629.7846 centred at (gu) : 89.69612 92.37398 90.34382 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6966 nv = 96 ne = 84 npr = 83370 no. pairs analyzed = 83370 no. exposed pairs = 5269 no. arc points = 36922 no. surface atoms = 1785 nbur = 2405 mkacc time = 0.2300000 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 = 1.652000 m= 240 mr = 3542 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 3654 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3604 ## 543 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 9212 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.2712432E-11 5.2029686E-11 midg,1,midg; midg,igrid,midg 3.5500710E-11 -1.4652353E-10 1,midg,midg; igrid,midg,midg 2.0681461E-10 -1.8096581E-10 gauss-seidel spectral radius is 0.9801469 estimated iterations to convergence 59 setup time was (sec) 0.7500000 now iterating at: 06:46:30 rms-change max change #iterations 5.9647553E-02 10.77280 at 10iterations 3.4028911E-03 0.5511026 at 20iterations 2.9233994E-04 3.9604187E-02 at 30iterations 5.1270854E-05 5.2947998E-03 at 40iterations 1.1071417E-05 1.1110306E-03 at 50iterations finished qdiffx linear iterations at : 06:46:33 total time elapsed so far: 4.170000 # loops : 50 mean,max change (kT/e) : 1.1071417E-05 1.1110306E-03 energy calculations done at 4.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.330000 DelPhi exited at 06:46:34 4.336u 0.238s 0:04.95 92.1% 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 Tue Oct 11 2011 at 06:46:34 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 = 4190 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: 1.523951 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): -7.616000 62.46500 ymin,ymax (A): -109.7220 -49.35900 zmin,zma (A): -113.5750 -65.34500 x,y,z range (A): 70.08100 60.36300 48.23000 scale (grids/A): 1.523951 object centre (A): 27.42450 -79.54050 -89.46001 number of atom coordinates read : 4190 total number of charged atoms : 4043 net assigned charge : -0.4999840 assigned positive charge : 629.2817 centred at (gu) : 88.80130 97.01405 91.10780 assigned negative charge : -629.7846 centred at (gu) : 89.08820 97.12167 91.03094 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 78273 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36922 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 21782 mr = 52769 m= 1730 mr = 14227 m= 40 mr = 677 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 215 time to turn everything in is 0.5900000 number of dielectric boundary points 34152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 477 ## 10 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 30356 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) : 0.5079836 object centre at (A) : 27.42450 -79.54050 -89.46001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.5436314E-05 1.6735290E-03 midg,1,midg; midg,igrid,midg -3.2967026E-03 -1.1135688E-02 1,midg,midg; igrid,midg,midg 4.6991806E-02 1.1350472E-02 gauss-seidel spectral radius is 0.9980230 estimated iterations to convergence 179 setup time was (sec) 0.9400000 now iterating at: 06:46:35 rms-change max change #iterations 3.439933 164.3689 at 10iterations 1.385263 60.63496 at 20iterations 0.5600824 21.42914 at 30iterations 0.2251206 7.578834 at 40iterations 9.0641923E-02 3.365791 at 50iterations 3.6628205E-02 1.322514 at 60iterations 1.4709705E-02 0.4782639 at 70iterations 5.9364773E-03 0.2013531 at 80iterations 2.4028081E-03 7.9170227E-02 at 90iterations 9.7502163E-04 3.2723427E-02 at 100iterations 3.9826852E-04 1.3501406E-02 at 110iterations 1.6495562E-04 5.7220459E-03 at 120iterations finished qdiffx linear iterations at : 06:46:44 total time elapsed so far: 9.670000 # loops : 120 mean,max change (kT/e) : 1.6495562E-04 5.7220459E-03 energy calculations done at 9.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.850000 DelPhi exited at 06:46:44 9.852u 0.291s 0:10.44 97.1% 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 Tue Oct 11 2011 at 06:46:45 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 = 4190 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: 2.285926 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): -7.616000 62.46500 ymin,ymax (A): -109.7220 -49.35900 zmin,zma (A): -113.5750 -65.34500 x,y,z range (A): 70.08100 60.36300 48.23000 scale (grids/A): 2.285926 object centre (A): 27.42450 -79.54050 -89.46001 number of atom coordinates read : 4190 total number of charged atoms : 4043 net assigned charge : -0.4999840 assigned positive charge : 629.2817 centred at (gu) : 88.20177 100.5210 91.66134 assigned negative charge : -629.7846 centred at (gu) : 88.63221 100.6823 91.54639 start vw surface at 0.1800000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 182344 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36922 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 78942 mr = 129581 m= 18867 mr = 61267 m= 2313 mr = 13458 m= 105 mr = 1357 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 735 time to turn everything in is 1.430000 number of dielectric boundary points 76884 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 72 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 32251 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) : 1.523951 object centre at (A) : 27.42450 -79.54050 -89.46001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9705457E-02 8.5753892E-03 midg,1,midg; midg,igrid,midg -4.4812780E-02 -0.1453069 1,midg,midg; igrid,midg,midg 1.058194 0.2247633 gauss-seidel spectral radius is 0.9991186 estimated iterations to convergence 266 setup time was (sec) 1.800000 now iterating at: 06:46:47 rms-change max change #iterations 9.445726 286.4348 at 10iterations 5.349917 141.4058 at 20iterations 2.996689 79.64564 at 30iterations 1.674780 38.79021 at 40iterations 0.9301745 20.31428 at 50iterations 0.5159700 11.68055 at 60iterations 0.2848948 6.199890 at 70iterations 0.1571812 3.160458 at 80iterations 8.6507320E-02 1.919725 at 90iterations 4.7535591E-02 1.061523 at 100iterations 2.6125345E-02 0.5774994 at 110iterations 1.4319039E-02 0.2865372 at 120iterations 7.8518754E-03 0.1537266 at 130iterations 4.2983852E-03 9.2532158E-02 at 140iterations 2.3548887E-03 4.7365189E-02 at 150iterations 1.2870237E-03 2.4209261E-02 at 160iterations 7.0534565E-04 1.3523102E-02 at 170iterations 3.8664145E-04 7.4481964E-03 at 180iterations finished qdiffx linear iterations at : 06:47:01 total time elapsed so far: 15.97000 # loops : 180 mean,max change (kT/e) : 3.8664145E-04 7.4481964E-03 energy calculations done at 15.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.16000 DelPhi exited at 06:47:01 16.158u 0.312s 0:16.91 97.3% 0+0k 0+0io 0pf+0w