Tue Oct 11 08:05:25 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 Tue Oct 11 2011 at 08:05:25 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2475 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5668699 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): -7.783000 36.75300 ymin,ymax (A): -15.64300 32.94200 zmin,zma (A): -10.36700 52.43400 x,y,z range (A): 44.53600 48.58500 62.80100 scale (grids/A): 0.5668699 object centre (A): 14.48500 8.649501 21.03350 number of atom coordinates read : 2475 total number of charged atoms : 2307 net assigned charge : 10.50002 assigned positive charge : 358.9199 centred at (gu) : 89.95563 90.68200 89.05950 assigned negative charge : -348.4207 centred at (gu) : 89.86659 90.76160 89.13381 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 5365 nv = 96 ne = 84 npr = 49081 no. pairs analyzed = 49081 no. exposed pairs = 3300 no. arc points = 23517 no. surface atoms = 1108 nbur = 1367 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 = 1.540000 m= 221 mr = 2681 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.3200000 number of dielectric boundary points 2900 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2368 ## 296 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 6722 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8122193E-09 4.9701010E-10 midg,1,midg; midg,igrid,midg 1.9653286E-09 6.3443206E-10 1,midg,midg; igrid,midg,midg 4.4633350E-10 2.3841182E-09 gauss-seidel spectral radius is 0.9839108 estimated iterations to convergence 65 setup time was (sec) 0.5500000 now iterating at: 08:05:26 rms-change max change #iterations 7.8126594E-02 14.78983 at 10iterations 5.6518870E-03 0.9534241 at 20iterations 4.1144452E-04 7.3024750E-02 at 30iterations 3.0489557E-05 4.7345161E-03 at 40iterations 2.2974214E-06 4.3773651E-04 at 50iterations finished qdiffx linear iterations at : 08:05:28 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 2.2974214E-06 4.3773651E-04 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 08:05:29 3.338u 0.157s 0:03.99 87.2% 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 Tue Oct 11 2011 at 08:05:29 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2475 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.700610 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): -7.783000 36.75300 ymin,ymax (A): -15.64300 32.94200 zmin,zma (A): -10.36700 52.43400 x,y,z range (A): 44.53600 48.58500 62.80100 scale (grids/A): 1.700610 object centre (A): 14.48500 8.649501 21.03350 number of atom coordinates read : 2475 total number of charged atoms : 2307 net assigned charge : 10.50002 assigned positive charge : 358.9199 centred at (gu) : 89.86663 92.04557 87.17792 assigned negative charge : -348.4207 centred at (gu) : 89.59977 92.28455 87.40130 start vw surface at 0.1600000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 58361 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23517 grid for indexing accessible points = 1.400000 m= 17765 mr = 38376 m= 1908 mr = 12039 m= 56 mr = 875 m= 0 mr = 2 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 197 time to turn everything in is 0.4500000 number of dielectric boundary points 26798 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 300 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 17873 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) : 0.5668699 object centre at (A) : 14.48500 8.649501 21.03350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5484828E-02 1.6985547E-02 midg,1,midg; midg,igrid,midg 8.0141388E-03 1.8831627E-03 1,midg,midg; igrid,midg,midg 3.5062158E-03 9.2338426E-03 gauss-seidel spectral radius is 0.9982837 estimated iterations to convergence 192 setup time was (sec) 0.7300000 now iterating at: 08:05:30 rms-change max change #iterations 3.156904 154.3205 at 10iterations 1.342741 54.07359 at 20iterations 0.5750590 24.05394 at 30iterations 0.2447159 10.06382 at 40iterations 0.1044644 3.697738 at 50iterations 4.4414259E-02 1.642247 at 60iterations 1.8891782E-02 0.6869411 at 70iterations 8.0686435E-03 0.3243163 at 80iterations 3.4431606E-03 0.1253338 at 90iterations 1.4717635E-03 5.8689356E-02 at 100iterations 6.2889734E-04 2.4391174E-02 at 110iterations 2.6814788E-04 9.7417831E-03 at 120iterations finished qdiffx linear iterations at : 08:05:36 total time elapsed so far: 7.060000 # loops : 120 mean,max change (kT/e) : 2.6814788E-04 9.7417831E-03 energy calculations done at 7.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.250000 DelPhi exited at 08:05:37 7.252u 0.163s 0:07.71 96.1% 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 Tue Oct 11 2011 at 08:05:37 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2475 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: 2.550915 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): -7.783000 36.75300 ymin,ymax (A): -15.64300 32.94200 zmin,zma (A): -10.36700 52.43400 x,y,z range (A): 44.53600 48.58500 62.80100 scale (grids/A): 2.550915 object centre (A): 14.48500 8.649501 21.03350 number of atom coordinates read : 2475 total number of charged atoms : 2307 net assigned charge : 10.50002 assigned positive charge : 358.9199 centred at (gu) : 89.79977 93.06830 85.76675 assigned negative charge : -348.4207 centred at (gu) : 89.39947 93.42676 86.10182 start vw surface at 0.1500000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 135358 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23517 grid for indexing accessible points = 1.400000 m= 61035 mr = 94009 m= 17631 mr = 47684 m= 2871 mr = 13055 m= 220 mr = 1805 m= 1 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 595 time to turn everything in is 1.040000 number of dielectric boundary points 60475 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 18444 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) : 1.700610 object centre at (A) : 14.48500 8.649501 21.03350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5001664 0.3881644 midg,1,midg; midg,igrid,midg 8.8035673E-02 5.0296001E-02 1,midg,midg; igrid,midg,midg 5.2385166E-02 0.1057160 gauss-seidel spectral radius is 0.9991595 estimated iterations to convergence 272 setup time was (sec) 1.330000 now iterating at: 08:05:38 rms-change max change #iterations 8.100835 276.3255 at 10iterations 4.611394 145.0385 at 20iterations 2.603801 63.47105 at 30iterations 1.462033 34.07246 at 40iterations 0.8136920 17.95683 at 50iterations 0.4558797 9.754077 at 60iterations 0.2531841 5.603566 at 70iterations 0.1413475 3.460236 at 80iterations 7.8187555E-02 1.845381 at 90iterations 4.3316197E-02 0.9872284 at 100iterations 2.3995651E-02 0.5875003 at 110iterations 1.3314525E-02 0.2953720 at 120iterations 7.3609864E-03 0.1523972 at 130iterations 4.0718135E-03 8.9080811E-02 at 140iterations 2.2545541E-03 5.1025391E-02 at 150iterations 1.2472725E-03 2.8144836E-02 at 160iterations 6.9014513E-04 1.5895844E-02 at 170iterations 3.8171976E-04 8.3980560E-03 at 180iterations finished qdiffx linear iterations at : 08:05:48 total time elapsed so far: 11.18000 # loops : 180 mean,max change (kT/e) : 3.8171976E-04 8.3980560E-03 energy calculations done at 11.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.36000 DelPhi exited at 08:05:49 11.362u 0.193s 0:11.94 96.7% 0+0k 0+0io 0pf+0w