Sat Oct 8 23:48:38 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 Sat Oct 8 2011 at 23:48:38 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3413 !!! WARNING: HIT 88 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5552869 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): -46.88300 7.271000 ymin,ymax (A): 176.7450 237.9000 zmin,zma (A): 78.67000 142.7810 x,y,z range (A): 54.15400 61.15500 64.11101 scale (grids/A): 0.5552869 object centre (A): -19.80600 207.3225 110.7255 number of atom coordinates read : 3413 total number of charged atoms : 3269 net assigned charge : 14.01402 assigned positive charge : 506.4233 centred at (gu) : 89.92096 89.31060 90.57674 assigned negative charge : -492.4113 centred at (gu) : 89.84341 89.24255 90.68293 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7107 nv = 96 ne = 84 npr = 66171 no. pairs analyzed = 66171 no. exposed pairs = 4647 no. arc points = 32537 no. surface atoms = 1547 nbur = 1866 mkacc time = 0.1200000 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 = 1.568000 m= 299 mr = 3527 m= 2 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.2300000 number of dielectric boundary points 3870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3298 ## 393 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9103 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0438868E-09 1.6090337E-10 midg,1,midg; midg,igrid,midg 6.4293659E-10 1.6632498E-09 1,midg,midg; igrid,midg,midg 4.5933213E-10 2.0196653E-09 gauss-seidel spectral radius is 0.9833201 estimated iterations to convergence 64 setup time was (sec) 0.4200000 now iterating at: 23:48:39 rms-change max change #iterations 8.6320274E-02 11.43940 at 10iterations 5.9993961E-03 0.9750137 at 20iterations 4.2646925E-04 7.1164131E-02 at 30iterations 3.5940757E-05 5.2701235E-03 at 40iterations 4.5686825E-06 6.1607361E-04 at 50iterations finished qdiffx linear iterations at : 23:48:42 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 4.5686825E-06 6.1607361E-04 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 23:48:42 3.390u 0.174s 0:03.84 92.7% 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 23:48:42 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3413 !!! WARNING: HIT 88 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.665861 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): -46.88300 7.271000 ymin,ymax (A): 176.7450 237.9000 zmin,zma (A): 78.67000 142.7810 x,y,z range (A): 54.15400 61.15500 64.11101 scale (grids/A): 1.665861 object centre (A): -19.80600 207.3225 110.7255 number of atom coordinates read : 3413 total number of charged atoms : 3269 net assigned charge : 14.01402 assigned positive charge : 506.4233 centred at (gu) : 89.76196 87.93093 91.72918 assigned negative charge : -492.4113 centred at (gu) : 89.53024 87.72733 92.04874 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 78291 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32537 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24557 mr = 52001 m= 2622 mr = 16459 m= 83 mr = 1247 m= 0 mr = 7 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 911 time to turn everything in is 0.3800000 number of dielectric boundary points 35839 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 332 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 25124 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) : 0.5552869 object centre at (A) : -19.80600 207.3225 110.7255 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1539501E-05 -6.0362034E-03 midg,1,midg; midg,igrid,midg 2.6420929E-02 2.6017914E-02 1,midg,midg; igrid,midg,midg 4.0437495E-03 1.6053572E-02 gauss-seidel spectral radius is 0.9983212 estimated iterations to convergence 194 setup time was (sec) 0.5900000 now iterating at: 23:48:43 rms-change max change #iterations 3.727239 187.1832 at 10iterations 1.597837 57.57545 at 20iterations 0.6874766 26.20721 at 30iterations 0.2956832 10.43748 at 40iterations 0.1272272 3.866940 at 50iterations 5.4680977E-02 1.860191 at 60iterations 2.3591770E-02 0.7711964 at 70iterations 1.0150537E-02 0.3404655 at 80iterations 4.3760496E-03 0.1401825 at 90iterations 1.8879279E-03 6.3745499E-02 at 100iterations 8.1541459E-04 2.5665998E-02 at 110iterations 3.5031320E-04 1.2042999E-02 at 120iterations finished qdiffx linear iterations at : 23:48:50 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 3.5031320E-04 1.2042999E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 23:48:51 7.835u 0.220s 0:08.42 95.6% 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 23:48:51 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3413 !!! WARNING: HIT 88 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.498791 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): -46.88300 7.271000 ymin,ymax (A): 176.7450 237.9000 zmin,zma (A): 78.67000 142.7810 x,y,z range (A): 54.15400 61.15500 64.11101 scale (grids/A): 2.498791 object centre (A): -19.80600 207.3225 110.7255 number of atom coordinates read : 3413 total number of charged atoms : 3269 net assigned charge : 14.01402 assigned positive charge : 506.4233 centred at (gu) : 89.64271 86.89619 92.59353 assigned negative charge : -492.4113 centred at (gu) : 89.29532 86.59094 93.07281 start vw surface at 0.1000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 181889 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32537 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 83626 mr = 127877 m= 24667 mr = 64946 m= 4236 mr = 18233 m= 338 mr = 2700 m= 8 mr = 140 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 3241 time to turn everything in is 0.9300000 number of dielectric boundary points 80868 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 26140 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) : 1.665861 object centre at (A) : -19.80600 207.3225 110.7255 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3649830 -8.0508113E-02 midg,1,midg; midg,igrid,midg 0.3510398 0.3906596 1,midg,midg; igrid,midg,midg 5.4259726E-04 0.1814779 gauss-seidel spectral radius is 0.9991985 estimated iterations to convergence 279 setup time was (sec) 1.180000 now iterating at: 23:48:52 rms-change max change #iterations 9.498019 279.3249 at 10iterations 5.495218 125.7130 at 20iterations 3.154786 72.56372 at 30iterations 1.799508 41.52583 at 40iterations 1.023565 21.58175 at 50iterations 0.5811380 12.47158 at 60iterations 0.3282489 6.536836 at 70iterations 0.1853665 3.625221 at 80iterations 0.1045597 2.074778 at 90iterations 5.8867104E-02 1.213396 at 100iterations 3.3094261E-02 0.6215553 at 110iterations 1.8608022E-02 0.3870449 at 120iterations 1.0464587E-02 0.1926198 at 130iterations 5.8703711E-03 0.1091213 at 140iterations 3.3078734E-03 6.7603588E-02 at 150iterations 1.8546348E-03 3.5474539E-02 at 160iterations 1.0428496E-03 1.8827438E-02 at 170iterations 5.8544928E-04 1.1035919E-02 at 180iterations finished qdiffx linear iterations at : 23:49:04 total time elapsed so far: 12.59000 # loops : 180 mean,max change (kT/e) : 5.8544928E-04 1.1035919E-02 energy calculations done at 12.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.72000 DelPhi exited at 23:49:04 12.724u 0.199s 0:13.20 97.8% 0+0k 0+0io 0pf+0w