Sat Oct 8 18:13:22 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 Sat Oct 8 2011 at 18:13:22 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 = 3382 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5306385 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): -9.971999 41.34400 ymin,ymax (A): -39.07700 28.01200 zmin,zma (A): -16.81300 34.04000 x,y,z range (A): 51.31600 67.08900 50.85300 scale (grids/A): 0.5306385 object centre (A): 15.68600 -5.532500 8.613499 number of atom coordinates read : 3382 total number of charged atoms : 3238 net assigned charge : 5.0365925E-06 assigned positive charge : 505.7745 centred at (gu) : 89.85634 91.55653 90.67069 assigned negative charge : -505.7759 centred at (gu) : 89.87492 91.50568 90.63848 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6018 nv = 96 ne = 84 npr = 70219 no. pairs analyzed = 70219 no. exposed pairs = 3891 no. arc points = 26839 no. surface atoms = 1334 nbur = 2048 mkacc time = 0.1100000 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 = 1.624000 m= 189 mr = 3336 m= 0 mr = 11 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 2860 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2701 ## 396 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 7946 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1775449E-10 1.5377241E-10 midg,1,midg; midg,igrid,midg -1.4677128E-10 3.0956035E-10 1,midg,midg; igrid,midg,midg 7.5407368E-11 -7.9631003E-11 gauss-seidel spectral radius is 0.9817210 estimated iterations to convergence 61 setup time was (sec) 0.4500000 now iterating at: 18:13:23 rms-change max change #iterations 6.8112768E-02 11.64948 at 10iterations 4.3588630E-03 0.7140722 at 20iterations 3.1195465E-04 4.8801422E-02 at 30iterations 4.0926159E-05 8.2621574E-03 at 40iterations 9.1917182E-06 1.9574165E-03 at 50iterations finished qdiffx linear iterations at : 18:13:26 total time elapsed so far: 3.540000 # loops : 50 mean,max change (kT/e) : 9.1917182E-06 1.9574165E-03 energy calculations done at 3.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.670000 DelPhi exited at 18:13:27 3.673u 0.196s 0:04.43 87.1% 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 Sat Oct 8 2011 at 18:13:27 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 = 3382 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.591915 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): -9.971999 41.34400 ymin,ymax (A): -39.07700 28.01200 zmin,zma (A): -16.81300 34.04000 x,y,z range (A): 51.31600 67.08900 50.85300 scale (grids/A): 1.591915 object centre (A): 15.68600 -5.532500 8.613499 number of atom coordinates read : 3382 total number of charged atoms : 3238 net assigned charge : 5.0365925E-06 assigned positive charge : 505.7745 centred at (gu) : 89.56831 94.66888 92.01111 assigned negative charge : -505.7759 centred at (gu) : 89.62427 94.51666 91.91521 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 67245 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26839 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 19892 mr = 47641 m= 1794 mr = 13738 m= 49 mr = 849 m= 0 mr = 2 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 223 time to turn everything in is 0.3400000 number of dielectric boundary points 26750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 357 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 24633 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) : 0.5306385 object centre at (A) : 15.68600 -5.532500 8.613499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5336178E-03 2.7761101E-03 midg,1,midg; midg,igrid,midg 6.0924683E-03 8.2983775E-03 1,midg,midg; igrid,midg,midg 3.5461215E-03 -1.8980860E-03 gauss-seidel spectral radius is 0.9981094 estimated iterations to convergence 183 setup time was (sec) 0.5800000 now iterating at: 18:13:27 rms-change max change #iterations 3.344980 165.9970 at 10iterations 1.378880 48.97986 at 20iterations 0.5654190 19.71141 at 30iterations 0.2321813 7.661312 at 40iterations 9.5456235E-02 3.739031 at 50iterations 3.9015252E-02 1.450235 at 60iterations 1.6037446E-02 0.5519409 at 70iterations 6.5775528E-03 0.2297926 at 80iterations 2.7199539E-03 9.0060234E-02 at 90iterations 1.1221702E-03 3.8608551E-02 at 100iterations 4.6317338E-04 1.5720367E-02 at 110iterations 1.9407648E-04 6.8054199E-03 at 120iterations finished qdiffx linear iterations at : 18:13:35 total time elapsed so far: 8.160000 # loops : 120 mean,max change (kT/e) : 1.9407648E-04 6.8054199E-03 energy calculations done at 8.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.290000 DelPhi exited at 18:13:35 8.293u 0.229s 0:08.80 96.7% 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 Sat Oct 8 2011 at 18:13:35 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 = 3382 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.387873 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): -9.971999 41.34400 ymin,ymax (A): -39.07700 28.01200 zmin,zma (A): -16.81300 34.04000 x,y,z range (A): 51.31600 67.08900 50.85300 scale (grids/A): 2.387873 object centre (A): 15.68600 -5.532500 8.613499 number of atom coordinates read : 3382 total number of charged atoms : 3238 net assigned charge : 5.0365925E-06 assigned positive charge : 505.7745 centred at (gu) : 89.35206 97.00307 93.01646 assigned negative charge : -505.7759 centred at (gu) : 89.43641 96.77502 92.87263 start vw surface at 0.1100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 156760 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26839 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 71287 mr = 116248 m= 18393 mr = 57193 m= 2773 mr = 13830 m= 164 mr = 1731 m= 2 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 727 time to turn everything in is 0.8200000 number of dielectric boundary points 60318 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 25859 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) : 1.591915 object centre at (A) : 15.68600 -5.532500 8.613499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.5275181E-02 6.0034078E-02 midg,1,midg; midg,igrid,midg 0.1694402 0.2030204 1,midg,midg; igrid,midg,midg 6.6152133E-02 -2.4060695E-02 gauss-seidel spectral radius is 0.9991141 estimated iterations to convergence 265 setup time was (sec) 1.080000 now iterating at: 18:13:37 rms-change max change #iterations 8.719858 263.1937 at 10iterations 4.837695 107.2048 at 20iterations 2.670620 62.09239 at 30iterations 1.469685 33.89872 at 40iterations 0.8072451 22.39970 at 50iterations 0.4427117 10.07581 at 60iterations 0.2424861 5.141064 at 70iterations 0.1328811 2.613602 at 80iterations 7.2440267E-02 1.516275 at 90iterations 3.9619297E-02 0.7810264 at 100iterations 2.1585939E-02 0.4094553 at 110iterations 1.1819657E-02 0.2240434 at 120iterations 6.4478535E-03 0.1274214 at 130iterations 3.5220461E-03 7.6759338E-02 at 140iterations 1.9219785E-03 3.8661957E-02 at 150iterations 1.0503622E-03 2.2131920E-02 at 160iterations 5.7540438E-04 1.1232376E-02 at 170iterations 3.1548334E-04 6.5450668E-03 at 180iterations finished qdiffx linear iterations at : 18:13:49 total time elapsed so far: 13.64000 # loops : 180 mean,max change (kT/e) : 3.1548334E-04 6.5450668E-03 energy calculations done at 13.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.77000 DelPhi exited at 18:13:50 13.773u 0.265s 0:14.35 97.7% 0+0k 0+0io 0pf+0w