Sat Mar 3 09:32:27 PST 2012 #!/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_thinner.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 Mar 3 2012 at 09:32:27 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3107 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5966647 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): 1.996000 61.66100 ymin,ymax (A): -21.70900 26.76200 zmin,zma (A): -9.971000 45.08700 x,y,z range (A): 59.66500 48.47100 55.05800 scale (grids/A): 0.5966647 object centre (A): 31.82850 2.526500 17.55800 number of atom coordinates read : 3107 total number of charged atoms : 2964 net assigned charge : 2.000008 assigned positive charge : 462.6611 centred at (gu) : 90.15092 89.28240 91.04976 assigned negative charge : -460.6622 centred at (gu) : 90.13934 89.23964 91.08188 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7248 nv = 96 ne = 84 npr = 64105 no. pairs analyzed = 64105 no. exposed pairs = 3646 no. arc points = 25846 no. surface atoms = 1211 nbur = 1896 mkacc time = 0.1700000 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 = 1.456000 m= 327 mr = 4035 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3500000 number of dielectric boundary points 3516 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2633 ## 286 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9240 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6099705E-09 -6.0292010E-10 midg,1,midg; midg,igrid,midg -1.0489737E-09 2.0836071E-09 1,midg,midg; igrid,midg,midg 3.3233663E-10 1.2887856E-09 gauss-seidel spectral radius is 0.9855024 estimated iterations to convergence 68 setup time was (sec) 0.6600000 now iterating at: 09:32:28 rms-change max change #iterations 0.1141874 20.10004 at 10iterations 1.1266186E-02 1.627110 at 20iterations 2.3364027E-03 0.5044479 at 30iterations 7.5933209E-04 0.1715851 at 40iterations 2.5930780E-04 5.8868408E-02 at 50iterations finished qdiffx linear iterations at : 09:32:32 total time elapsed so far: 4.800000 # loops : 50 mean,max change (kT/e) : 2.5930780E-04 5.8868408E-02 energy calculations done at 4.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.970000 DelPhi exited at 09:32:33 4.971u 0.375s 0:05.62 95.0% 0+0k 0+0io 6pf+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 Mar 3 2012 at 09:32:33 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3107 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.789994 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): 1.996000 61.66100 ymin,ymax (A): -21.70900 26.76200 zmin,zma (A): -9.971000 45.08700 x,y,z range (A): 59.66500 48.47100 55.05800 scale (grids/A): 1.789994 object centre (A): 31.82850 2.526500 17.55800 number of atom coordinates read : 3107 total number of charged atoms : 2964 net assigned charge : 2.000008 assigned positive charge : 462.6611 centred at (gu) : 90.45168 87.84671 93.14866 assigned negative charge : -460.6622 centred at (gu) : 90.41774 87.71844 93.24532 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 80072 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25846 grid for indexing accessible points = 1.400000 m= 26947 mr = 56721 m= 3283 mr = 19496 m= 136 mr = 1866 m= 0 mr = 34 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 433 time to turn everything in is 0.6400000 number of dielectric boundary points 32321 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 216 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 23081 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) : 0.5966647 object centre at (A) : 31.82850 2.526500 17.55800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.8757109E-03 -1.8612767E-02 midg,1,midg; midg,igrid,midg -2.7006839E-03 7.8854449E-03 1,midg,midg; igrid,midg,midg 2.8478445E-02 1.2200829E-02 gauss-seidel spectral radius is 0.9985073 estimated iterations to convergence 205 setup time was (sec) 0.9500000 now iterating at: 09:32:34 rms-change max change #iterations 4.109576 179.6873 at 10iterations 1.847720 62.97393 at 20iterations 0.8387932 30.08362 at 30iterations 0.3796352 14.16436 at 40iterations 0.1729409 5.680708 at 50iterations 7.8528345E-02 2.557829 at 60iterations 3.5982903E-02 1.222183 at 70iterations 1.6752513E-02 0.5677109 at 80iterations 7.9346867E-03 0.2817421 at 90iterations 3.9610555E-03 0.1534119 at 100iterations 2.1244355E-03 8.2595825E-02 at 110iterations 1.2238825E-03 5.1895142E-02 at 120iterations finished qdiffx linear iterations at : 09:32:45 total time elapsed so far: 11.84000 # loops : 120 mean,max change (kT/e) : 1.2238825E-03 5.1895142E-02 energy calculations done at 11.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.01000 DelPhi exited at 09:32:46 12.010u 0.438s 0:12.72 97.7% 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 Mar 3 2012 at 09:32:46 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3107 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.684991 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): 1.996000 61.66100 ymin,ymax (A): -21.70900 26.76200 zmin,zma (A): -9.971000 45.08700 x,y,z range (A): 59.66500 48.47100 55.05800 scale (grids/A): 2.684991 object centre (A): 31.82850 2.526500 17.55800 number of atom coordinates read : 3107 total number of charged atoms : 2964 net assigned charge : 2.000008 assigned positive charge : 462.6611 centred at (gu) : 90.67754 86.76971 94.72274 assigned negative charge : -460.6622 centred at (gu) : 90.62658 86.57757 94.86781 start vw surface at 0.1200000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 186169 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25846 grid for indexing accessible points = 1.400000 m= 91065 mr = 138010 m= 28266 mr = 74245 m= 5503 mr = 22162 m= 572 mr = 3995 m= 23 mr = 331 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 1611 time to turn everything in is 1.620000 number of dielectric boundary points 72846 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 23710 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) : 1.789994 object centre at (A) : 31.82850 2.526500 17.55800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.5519274E-02 -0.1544915 midg,1,midg; midg,igrid,midg -4.8408452E-02 0.1079108 1,midg,midg; igrid,midg,midg 0.5416936 0.1956664 gauss-seidel spectral radius is 0.9992313 estimated iterations to convergence 285 setup time was (sec) 1.960000 now iterating at: 09:32:48 rms-change max change #iterations 9.901404 341.2431 at 10iterations 5.711161 117.6383 at 20iterations 3.284935 64.41073 at 30iterations 1.885781 38.13228 at 40iterations 1.075839 20.74343 at 50iterations 0.6157656 11.43056 at 60iterations 0.3513836 7.012899 at 70iterations 0.2004104 3.838514 at 80iterations 0.1142814 2.327812 at 90iterations 6.5048210E-02 1.196712 at 100iterations 3.7135407E-02 0.6596522 at 110iterations 2.1280067E-02 0.3877192 at 120iterations 1.2234365E-02 0.2210388 at 130iterations 7.1229008E-03 0.1298828 at 140iterations 4.2335447E-03 8.6242676E-02 at 150iterations 2.5993774E-03 5.3260803E-02 at 160iterations 1.6651740E-03 4.0142059E-02 at 170iterations 1.1262085E-03 2.7853012E-02 at 180iterations finished qdiffx linear iterations at : 09:33:06 total time elapsed so far: 19.77000 # loops : 180 mean,max change (kT/e) : 1.1262085E-03 2.7853012E-02 energy calculations done at 19.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.94000 DelPhi exited at 09:33:06 19.945u 0.462s 0:20.68 98.6% 0+0k 0+0io 0pf+0w