Mon Oct 10 17:04:26 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 Mon Oct 10 2011 at 17:04:26 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2534 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6118626 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): 17.88200 70.68999 ymin,ymax (A): -37.41600 8.590000 zmin,zma (A): -26.28000 31.90300 x,y,z range (A): 52.80799 46.00600 58.18300 scale (grids/A): 0.6118626 object centre (A): 44.28600 -14.41300 2.811500 number of atom coordinates read : 2534 total number of charged atoms : 2398 net assigned charge : 3.500013 assigned positive charge : 374.7580 centred at (gu) : 91.17312 89.30299 89.24230 assigned negative charge : -371.2585 centred at (gu) : 91.18309 89.37586 89.33947 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6485 nv = 96 ne = 84 npr = 50102 no. pairs analyzed = 50102 no. exposed pairs = 3543 no. arc points = 24948 no. surface atoms = 1183 nbur = 1351 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 347 mr = 3309 m= 0 mr = 27 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.1900000 number of dielectric boundary points 3496 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2438 ## 251 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7848 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.2112237E-09 -2.3270543E-09 midg,1,midg; midg,igrid,midg 6.7042034E-09 -1.3038953E-09 1,midg,midg; igrid,midg,midg 2.0364288E-09 2.0886450E-09 gauss-seidel spectral radius is 0.9861753 estimated iterations to convergence 70 setup time was (sec) 0.4200000 now iterating at: 17:04:27 rms-change max change #iterations 0.1121619 17.88313 at 10iterations 1.0020407E-02 1.568607 at 20iterations 9.1378100E-04 0.1415024 at 30iterations 9.1642258E-05 1.5441895E-02 at 40iterations 1.1837290E-05 1.9264221E-03 at 50iterations finished qdiffx linear iterations at : 17:04:30 total time elapsed so far: 3.610000 # loops : 50 mean,max change (kT/e) : 1.1837290E-05 1.9264221E-03 energy calculations done at 3.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.740000 DelPhi exited at 17:04:31 3.743u 0.215s 0:04.86 81.2% 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 Mon Oct 10 2011 at 17:04:31 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 = 2534 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.835588 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): 17.88200 70.68999 ymin,ymax (A): -37.41600 8.590000 zmin,zma (A): -26.28000 31.90300 x,y,z range (A): 52.80799 46.00600 58.18300 scale (grids/A): 1.835588 object centre (A): 44.28600 -14.41300 2.811500 number of atom coordinates read : 2534 total number of charged atoms : 2398 net assigned charge : 3.500013 assigned positive charge : 374.7580 centred at (gu) : 93.51894 87.90857 87.72675 assigned negative charge : -371.2585 centred at (gu) : 93.54896 88.12741 88.01797 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 69746 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24948 grid for indexing accessible points = 1.400000 m= 24517 mr = 45966 m= 3669 mr = 17319 m= 168 mr = 2124 m= 3 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 32658 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 197 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 18789 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) : 0.6118626 object centre at (A) : 44.28600 -14.41300 2.811500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6520252E-02 -1.8239146E-02 midg,1,midg; midg,igrid,midg 1.7087040E-02 -2.7406665E-03 1,midg,midg; igrid,midg,midg 2.0848470E-02 8.1541752E-03 gauss-seidel spectral radius is 0.9985399 estimated iterations to convergence 208 setup time was (sec) 0.6000000 now iterating at: 17:04:32 rms-change max change #iterations 3.849805 162.8668 at 10iterations 1.749254 68.77870 at 20iterations 0.7985682 28.69853 at 30iterations 0.3626679 12.74143 at 40iterations 0.1648818 5.739340 at 50iterations 7.5311691E-02 2.311363 at 60iterations 3.4255255E-02 1.127540 at 70iterations 1.5626522E-02 0.5831833 at 80iterations 7.0949513E-03 0.2315264 at 90iterations 3.2383536E-03 0.1154871 at 100iterations 1.4790933E-03 5.3593397E-02 at 110iterations 6.7644165E-04 2.1916389E-02 at 120iterations finished qdiffx linear iterations at : 17:04:41 total time elapsed so far: 8.990000 # loops : 120 mean,max change (kT/e) : 6.7644165E-04 2.1916389E-02 energy calculations done at 8.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.120000 DelPhi exited at 17:04:42 9.124u 0.251s 0:10.29 91.0% 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 Mon Oct 10 2011 at 17:04:42 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2534 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.753382 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): 17.88200 70.68999 ymin,ymax (A): -37.41600 8.590000 zmin,zma (A): -26.28000 31.90300 x,y,z range (A): 52.80799 46.00600 58.18300 scale (grids/A): 2.753382 object centre (A): 44.28600 -14.41300 2.811500 number of atom coordinates read : 2534 total number of charged atoms : 2398 net assigned charge : 3.500013 assigned positive charge : 374.7580 centred at (gu) : 95.27848 86.86267 86.58996 assigned negative charge : -371.2585 centred at (gu) : 95.32345 87.19102 87.02684 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 161111 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24948 grid for indexing accessible points = 1.400000 m= 78927 mr = 112000 m= 28065 mr = 62501 m= 6325 mr = 22105 m= 701 mr = 4533 m= 23 mr = 369 m= 0 mr = 6 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9100000 number of dielectric boundary points 73638 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 19183 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) : 1.835588 object centre at (A) : 44.28600 -14.41300 2.811500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5295925 -8.6987289E-03 midg,1,midg; midg,igrid,midg 0.2351016 -1.3625582E-02 1,midg,midg; igrid,midg,midg 0.1849645 2.6765050E-02 gauss-seidel spectral radius is 0.9992470 estimated iterations to convergence 288 setup time was (sec) 1.180000 now iterating at: 17:04:43 rms-change max change #iterations 9.290592 308.4623 at 10iterations 5.445019 138.4305 at 20iterations 3.161301 75.56065 at 30iterations 1.830935 41.42600 at 40iterations 1.057919 22.50627 at 50iterations 0.6108559 15.56571 at 60iterations 0.3504587 7.190810 at 70iterations 0.2012545 4.351765 at 80iterations 0.1155212 2.308182 at 90iterations 6.6297524E-02 1.259501 at 100iterations 3.7933875E-02 0.7476356 at 110iterations 2.1701235E-02 0.4045162 at 120iterations 1.2443335E-02 0.2620077 at 130iterations 7.1233222E-03 0.1361194 at 140iterations 4.0772157E-03 7.6583862E-02 at 150iterations 2.3370984E-03 4.5866966E-02 at 160iterations 1.3378820E-03 2.5951385E-02 at 170iterations 7.6956500E-04 1.6590118E-02 at 180iterations finished qdiffx linear iterations at : 17:04:56 total time elapsed so far: 13.52000 # loops : 180 mean,max change (kT/e) : 7.6956500E-04 1.6590118E-02 energy calculations done at 13.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.64000 DelPhi exited at 17:04:56 13.645u 0.252s 0:14.82 93.7% 0+0k 0+0io 0pf+0w