Tue Oct 11 05:14:11 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 Tue Oct 11 2011 at 05:14:11 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2064 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.7090080 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): -19.75300 26.49500 ymin,ymax (A): -10.73400 28.40300 zmin,zma (A): -2.631000 47.58000 x,y,z range (A): 46.24800 39.13700 50.21100 scale (grids/A): 0.7090080 object centre (A): 3.370999 8.834500 22.47450 number of atom coordinates read : 2064 total number of charged atoms : 1930 net assigned charge : 5.945010 assigned positive charge : 315.5381 centred at (gu) : 89.29750 89.29390 90.10616 assigned negative charge : -309.5931 centred at (gu) : 89.16031 89.31856 90.14569 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7022 nv = 96 ne = 84 npr = 41425 no. pairs analyzed = 41425 no. exposed pairs = 2565 no. arc points = 17122 no. surface atoms = 876 nbur = 1188 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 451 mr = 4051 m= 1 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3343 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1557 ## 146 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7732 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.1086056E-08 3.3019717E-08 midg,1,midg; midg,igrid,midg 7.4407851E-08 3.5143344E-08 1,midg,midg; igrid,midg,midg -2.1313410E-08 1.0585661E-07 gauss-seidel spectral radius is 0.9896266 estimated iterations to convergence 80 setup time was (sec) 0.5700000 now iterating at: 05:14:12 rms-change max change #iterations 0.2054699 28.98629 at 10iterations 2.5926556E-02 3.495010 at 20iterations 3.3800718E-03 0.5118713 at 30iterations 5.3709885E-04 8.1912994E-02 at 40iterations 1.1868991E-04 1.3789177E-02 at 50iterations finished qdiffx linear iterations at : 05:14:15 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 1.1868991E-04 1.3789177E-02 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 05:14:16 4.084u 0.260s 0:04.77 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 Tue Oct 11 2011 at 05:14:16 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2064 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.127024 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): -19.75300 26.49500 ymin,ymax (A): -10.73400 28.40300 zmin,zma (A): -2.631000 47.58000 x,y,z range (A): 46.24800 39.13700 50.21100 scale (grids/A): 2.127024 object centre (A): 3.370999 8.834500 22.47450 number of atom coordinates read : 2064 total number of charged atoms : 1930 net assigned charge : 5.945010 assigned positive charge : 315.5381 centred at (gu) : 87.89249 87.88183 90.31836 assigned negative charge : -309.5931 centred at (gu) : 87.48093 87.95556 90.43713 start vw surface at 0.1300000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 74291 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17122 grid for indexing accessible points = 1.400000 m= 29818 mr = 52848 m= 5700 mr = 22661 m= 533 mr = 3847 m= 14 mr = 238 m= 0 mr = 3 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6800000 number of dielectric boundary points 30759 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 80 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 15337 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) : 0.7090080 object centre at (A) : 3.370999 8.834500 22.47450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6955230E-02 5.8436643E-02 midg,1,midg; midg,igrid,midg 3.3938289E-02 3.7630119E-03 1,midg,midg; igrid,midg,midg 3.7578985E-03 3.3334274E-02 gauss-seidel spectral radius is 0.9988322 estimated iterations to convergence 232 setup time was (sec) 0.9800000 now iterating at: 05:14:17 rms-change max change #iterations 4.646262 180.7374 at 10iterations 2.310030 81.77664 at 20iterations 1.146884 38.99749 at 30iterations 0.5694728 19.34681 at 40iterations 0.2841414 8.364676 at 50iterations 0.1403500 4.625206 at 60iterations 6.9748074E-02 1.973728 at 70iterations 3.4799982E-02 1.134743 at 80iterations 1.7393345E-02 0.5792313 at 90iterations 8.7031564E-03 0.2736588 at 100iterations 4.3893601E-03 0.1449442 at 110iterations 2.2501913E-03 6.2875032E-02 at 120iterations finished qdiffx linear iterations at : 05:14:26 total time elapsed so far: 9.380000 # loops : 120 mean,max change (kT/e) : 2.2501913E-03 6.2875032E-02 energy calculations done at 9.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.570000 DelPhi exited at 05:14:26 9.568u 0.321s 0:10.32 95.7% 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 Tue Oct 11 2011 at 05:14:26 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2064 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 3.190536 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): -19.75300 26.49500 ymin,ymax (A): -10.73400 28.40300 zmin,zma (A): -2.631000 47.58000 x,y,z range (A): 46.24800 39.13700 50.21100 scale (grids/A): 3.190536 object centre (A): 3.370999 8.834500 22.47450 number of atom coordinates read : 2064 total number of charged atoms : 1930 net assigned charge : 5.945010 assigned positive charge : 315.5381 centred at (gu) : 86.83866 86.82249 90.47764 assigned negative charge : -309.5931 centred at (gu) : 86.22137 86.93336 90.65574 start vw surface at 0.1400000 fill in re-entrant regions at 0.9700000 boundary points on vw surface= 171324 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17122 grid for indexing accessible points = 1.400000 m= 92849 mr = 127371 m= 37740 mr = 77241 m= 10908 mr = 31113 m= 2048 mr = 8398 m= 203 mr = 1485 m= 6 mr = 125 m= 0 mr = 3 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.190000 number of dielectric boundary points 69342 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.350000 number of grid points assigned charge 15440 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) : 2.127024 object centre at (A) : 3.370999 8.834500 22.47450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3298724 0.9518025 midg,1,midg; midg,igrid,midg 0.2737497 -1.2798896E-02 1,midg,midg; igrid,midg,midg 0.1377122 0.2702839 gauss-seidel spectral radius is 0.9992939 estimated iterations to convergence 297 setup time was (sec) 2.530000 now iterating at: 05:14:29 rms-change max change #iterations 10.31594 380.6770 at 10iterations 6.106978 133.0221 at 20iterations 3.587084 76.38004 at 30iterations 2.108688 41.68658 at 40iterations 1.237725 21.15429 at 50iterations 0.7280913 14.31826 at 60iterations 0.4264621 8.895710 at 70iterations 0.2497359 4.351759 at 80iterations 0.1459706 2.682703 at 90iterations 8.5648894E-02 1.582684 at 100iterations 5.0147023E-02 0.8880936 at 110iterations 2.9496679E-02 0.5464821 at 120iterations 1.7504843E-02 0.2953148 at 130iterations 1.0506906E-02 0.2041626 at 140iterations 6.4751399E-03 0.1440926 at 150iterations 4.1128686E-03 8.0574036E-02 at 160iterations 2.7628727E-03 5.0506592E-02 at 170iterations 1.9621039E-03 4.2343140E-02 at 180iterations finished qdiffx linear iterations at : 05:14:43 total time elapsed so far: 16.42000 # loops : 180 mean,max change (kT/e) : 1.9621039E-03 4.2343140E-02 energy calculations done at 16.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.61000 DelPhi exited at 05:14:44 16.610u 0.300s 0:17.45 96.9% 0+0k 0+0io 0pf+0w