Sun Oct 9 15:55:59 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 15:55:59 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5173 !!! WARNING: HIR 669 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5134863 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): 25.43700 85.72000 ymin,ymax (A): -83.37900 -14.04900 zmin,zma (A): -29.35800 38.25700 x,y,z range (A): 60.28300 69.32999 67.61500 scale (grids/A): 0.5134863 object centre (A): 55.57850 -48.71400 4.449500 number of atom coordinates read : 5173 total number of charged atoms : 5004 net assigned charge : -0.4859637 assigned positive charge : 792.7949 centred at (gu) : 90.76023 89.89649 89.04777 assigned negative charge : -793.2874 centred at (gu) : 90.68114 89.84470 89.00240 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8768 nv = 96 ne = 84 npr = 102154 no. pairs analyzed = 102154 no. exposed pairs = 6308 no. arc points = 44091 no. surface atoms = 2125 nbur = 3048 mkacc time = 0.1800000 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= 302 mr = 4718 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3500000 number of dielectric boundary points 4344 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4231 ## 598 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 11576 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0212837E-10 1.0765535E-10 midg,1,midg; midg,igrid,midg -1.8285433E-10 1.5491571E-10 1,midg,midg; igrid,midg,midg -2.1933041E-10 3.0218855E-10 gauss-seidel spectral radius is 0.9806319 estimated iterations to convergence 59 setup time was (sec) 0.5400000 now iterating at: 15:56:00 rms-change max change #iterations 7.1835272E-02 10.37641 at 10iterations 6.7854314E-03 0.9935684 at 20iterations 2.6337078E-03 0.4344864 at 30iterations 1.2628948E-03 0.2092094 at 40iterations 6.0818484E-04 0.1012154 at 50iterations finished qdiffx linear iterations at : 15:56:03 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 6.0818484E-04 0.1012154 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 15:56:03 3.568u 0.169s 0:04.12 90.2% 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 Sun Oct 9 2011 at 15:56:04 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5173 !!! WARNING: HIR 669 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.540459 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): 25.43700 85.72000 ymin,ymax (A): -83.37900 -14.04900 zmin,zma (A): -29.35800 38.25700 x,y,z range (A): 60.28300 69.32999 67.61500 scale (grids/A): 1.540459 object centre (A): 55.57850 -48.71400 4.449500 number of atom coordinates read : 5173 total number of charged atoms : 5004 net assigned charge : -0.4859637 assigned positive charge : 792.7949 centred at (gu) : 92.27898 89.68796 87.14162 assigned negative charge : -793.2874 centred at (gu) : 92.04357 89.53407 87.00700 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 99153 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44091 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 31561 mr = 69498 m= 3124 mr = 22045 m= 50 mr = 1488 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1700 time to turn everything in is 0.4800000 number of dielectric boundary points 40856 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 581 ## 12 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 37633 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) : 0.5134863 object centre at (A) : 55.57850 -48.71400 4.449500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7070420E-03 5.5670610E-04 midg,1,midg; midg,igrid,midg -1.7059552E-02 2.3617916E-02 1,midg,midg; igrid,midg,midg -8.3223507E-03 1.5739696E-02 gauss-seidel spectral radius is 0.9981734 estimated iterations to convergence 186 setup time was (sec) 0.7100000 now iterating at: 15:56:04 rms-change max change #iterations 4.096734 191.0878 at 10iterations 1.705682 64.10666 at 20iterations 0.7090344 26.70439 at 30iterations 0.2952699 8.790480 at 40iterations 0.1236005 3.636560 at 50iterations 5.1838610E-02 1.569275 at 60iterations 2.2274490E-02 0.7414277 at 70iterations 1.0115859E-02 0.3259468 at 80iterations 5.2323034E-03 0.1929207 at 90iterations 3.2188611E-03 0.1187134 at 100iterations 2.2627695E-03 7.9143524E-02 at 110iterations 1.6957110E-03 5.7971954E-02 at 120iterations finished qdiffx linear iterations at : 15:56:12 total time elapsed so far: 7.900000 # loops : 120 mean,max change (kT/e) : 1.6957110E-03 5.7971954E-02 energy calculations done at 7.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.030000 DelPhi exited at 15:56:12 8.034u 0.202s 0:08.56 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 15:56:12 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5173 !!! WARNING: HIR 669 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.310688 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): 25.43700 85.72000 ymin,ymax (A): -83.37900 -14.04900 zmin,zma (A): -29.35800 38.25700 x,y,z range (A): 60.28300 69.32999 67.61500 scale (grids/A): 2.310688 object centre (A): 55.57850 -48.71400 4.449500 number of atom coordinates read : 5173 total number of charged atoms : 5004 net assigned charge : -0.4859637 assigned positive charge : 792.7949 centred at (gu) : 93.41831 89.53158 85.71221 assigned negative charge : -793.2874 centred at (gu) : 93.06525 89.30110 85.51044 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 230803 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44091 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 109815 mr = 169976 m= 30989 mr = 87800 m= 4595 mr = 23344 m= 230 mr = 2967 m= 5 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.6999999 no. cavity mid-points inaccessible to solvent = 6111 time to turn everything in is 1.200000 number of dielectric boundary points 92288 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 64 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 39922 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) : 1.540459 object centre at (A) : 55.57850 -48.71400 4.449500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5876647E-02 4.4935748E-02 midg,1,midg; midg,igrid,midg -0.3236893 0.4407366 1,midg,midg; igrid,midg,midg -0.1055048 0.3613320 gauss-seidel spectral radius is 0.9991866 estimated iterations to convergence 277 setup time was (sec) 1.450000 now iterating at: 15:56:14 rms-change max change #iterations 11.02157 302.2784 at 10iterations 6.368492 154.0581 at 20iterations 3.640380 76.87939 at 30iterations 2.073360 49.20009 at 40iterations 1.177872 24.93621 at 50iterations 0.6646933 12.15396 at 60iterations 0.3748317 6.830307 at 70iterations 0.2116693 3.816867 at 80iterations 0.1187961 2.517878 at 90iterations 6.6912778E-02 1.247723 at 100iterations 3.7620209E-02 0.6893959 at 110iterations 2.1188986E-02 0.3962746 at 120iterations 1.2011727E-02 0.2088122 at 130iterations 6.8756104E-03 0.1282654 at 140iterations 4.0342286E-03 7.9551697E-02 at 150iterations 2.4649939E-03 4.6958923E-02 at 160iterations 1.6187304E-03 3.7790298E-02 at 170iterations 1.1547228E-03 2.4116516E-02 at 180iterations finished qdiffx linear iterations at : 15:56:26 total time elapsed so far: 13.19000 # loops : 180 mean,max change (kT/e) : 1.1547228E-03 2.4116516E-02 energy calculations done at 13.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.31000 DelPhi exited at 15:56:26 13.307u 0.221s 0:13.93 97.0% 0+0k 0+0io 0pf+0w