Mon Oct 10 19:38:06 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 Mon Oct 10 2011 at 19:38:06 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2441 !!! WARNING: HIR 86 has a net charge of 0.5140 !!! WARNING: HIR 257 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6101741 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): -11.15500 47.18900 ymin,ymax (A): 61.83600 114.4360 zmin,zma (A): 43.18000 86.89000 x,y,z range (A): 58.34400 52.60001 43.71000 scale (grids/A): 0.6101741 object centre (A): 18.01700 88.13600 65.03500 number of atom coordinates read : 2441 total number of charged atoms : 2302 net assigned charge : 2.8007582E-02 assigned positive charge : 369.7027 centred at (gu) : 87.90412 90.75253 91.20815 assigned negative charge : -369.6755 centred at (gu) : 87.96685 90.84518 91.34495 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6023 nv = 96 ne = 84 npr = 49764 no. pairs analyzed = 49764 no. exposed pairs = 2998 no. arc points = 20782 no. surface atoms = 999 nbur = 1442 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 293 mr = 3338 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.2800000 number of dielectric boundary points 2951 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2057 ## 205 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7463 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.8814179E-09 -8.5203338E-09 midg,1,midg; midg,igrid,midg 3.7023700E-09 -5.1377822E-09 1,midg,midg; igrid,midg,midg 4.8777040E-09 -1.8046549E-09 gauss-seidel spectral radius is 0.9860782 estimated iterations to convergence 69 setup time was (sec) 0.5400000 now iterating at: 19:38:06 rms-change max change #iterations 0.1149757 18.61910 at 10iterations 1.0210927E-02 1.546508 at 20iterations 9.2341221E-04 0.1449127 at 30iterations 8.8098430E-05 1.3622284E-02 at 40iterations 1.0795618E-05 1.8310547E-03 at 50iterations finished qdiffx linear iterations at : 19:38:10 total time elapsed so far: 3.970000 # loops : 50 mean,max change (kT/e) : 1.0795618E-05 1.8310547E-03 energy calculations done at 3.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.150000 DelPhi exited at 19:38:10 4.156u 0.232s 0:04.66 93.9% 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 Mon Oct 10 2011 at 19:38:10 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2441 !!! WARNING: HIR 86 has a net charge of 0.5140 !!! WARNING: HIR 257 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.830522 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): -11.15500 47.18900 ymin,ymax (A): 61.83600 114.4360 zmin,zma (A): 43.18000 86.89000 x,y,z range (A): 58.34400 52.60001 43.71000 scale (grids/A): 1.830522 object centre (A): 18.01700 88.13600 65.03500 number of atom coordinates read : 2441 total number of charged atoms : 2302 net assigned charge : 2.8007582E-02 assigned positive charge : 369.7027 centred at (gu) : 83.71172 92.25685 93.62391 assigned negative charge : -369.6755 centred at (gu) : 83.90031 92.53556 94.03447 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 65717 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20782 grid for indexing accessible points = 1.400000 m= 22675 mr = 46079 m= 3251 mr = 16630 m= 140 mr = 1959 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 972 time to turn everything in is 0.5200000 number of dielectric boundary points 27091 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 18018 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) : 0.6101741 object centre at (A) : 18.01700 88.13600 65.03500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0616537E-02 -1.2836148E-02 midg,1,midg; midg,igrid,midg 3.0790966E-02 -1.1708288E-02 1,midg,midg; igrid,midg,midg -2.0544985E-02 -9.1681546E-03 gauss-seidel spectral radius is 0.9985018 estimated iterations to convergence 205 setup time was (sec) 0.8600000 now iterating at: 19:38:11 rms-change max change #iterations 3.824627 156.5141 at 10iterations 1.723120 73.13356 at 20iterations 0.7811851 27.40360 at 30iterations 0.3531850 12.18841 at 40iterations 0.1591782 5.634660 at 50iterations 7.1975291E-02 2.597672 at 60iterations 3.2501269E-02 1.211862 at 70iterations 1.4706271E-02 0.4979248 at 80iterations 6.6676112E-03 0.2100067 at 90iterations 3.0241495E-03 9.8060071E-02 at 100iterations 1.3725695E-03 4.8393250E-02 at 110iterations 6.2308490E-04 2.3383141E-02 at 120iterations finished qdiffx linear iterations at : 19:38:20 total time elapsed so far: 9.250000 # loops : 120 mean,max change (kT/e) : 6.2308490E-04 2.3383141E-02 energy calculations done at 9.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.430000 DelPhi exited at 19:38:21 9.433u 0.276s 0:10.19 95.1% 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 Mon Oct 10 2011 at 19:38:21 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2441 !!! WARNING: HIR 86 has a net charge of 0.5140 !!! WARNING: HIR 257 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.745784 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): -11.15500 47.18900 ymin,ymax (A): 61.83600 114.4360 zmin,zma (A): 43.18000 86.89000 x,y,z range (A): 58.34400 52.60001 43.71000 scale (grids/A): 2.745784 object centre (A): 18.01700 88.13600 65.03500 number of atom coordinates read : 2441 total number of charged atoms : 2302 net assigned charge : 2.8007582E-02 assigned positive charge : 369.7027 centred at (gu) : 80.56738 93.38499 95.43575 assigned negative charge : -369.6755 centred at (gu) : 80.85037 93.80328 96.05167 start vw surface at 0.1400000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 152438 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20782 grid for indexing accessible points = 1.400000 m= 74750 mr = 111960 m= 25733 mr = 61276 m= 5691 mr = 20434 m= 604 mr = 4172 m= 16 mr = 331 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 3335 time to turn everything in is 1.290000 number of dielectric boundary points 61059 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 18414 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) : 1.830522 object centre at (A) : 18.01700 88.13600 65.03500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1286859 -0.1083923 midg,1,midg; midg,igrid,midg 0.4763980 -0.2245768 1,midg,midg; igrid,midg,midg -0.3052479 7.9631738E-02 gauss-seidel spectral radius is 0.9992165 estimated iterations to convergence 282 setup time was (sec) 1.660000 now iterating at: 19:38:23 rms-change max change #iterations 9.189252 336.7875 at 10iterations 5.299264 130.0060 at 20iterations 3.026897 70.41916 at 30iterations 1.728506 42.66539 at 40iterations 0.9826231 20.63068 at 50iterations 0.5577925 11.73356 at 60iterations 0.3162118 6.248211 at 70iterations 0.1793530 3.489641 at 80iterations 0.1014723 2.019772 at 90iterations 5.7395358E-02 1.057426 at 100iterations 3.2527819E-02 0.6131582 at 110iterations 1.8397702E-02 0.3761301 at 120iterations 1.0423978E-02 0.2092323 at 130iterations 5.8756550E-03 0.1186557 at 140iterations 3.3327178E-03 6.2578201E-02 at 150iterations 1.8829416E-03 3.8353920E-02 at 160iterations 1.0627627E-03 1.9445419E-02 at 170iterations 6.0200179E-04 1.1360168E-02 at 180iterations finished qdiffx linear iterations at : 19:38:37 total time elapsed so far: 16.06000 # loops : 180 mean,max change (kT/e) : 6.0200179E-04 1.1360168E-02 energy calculations done at 16.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.28000 DelPhi exited at 19:38:38 16.278u 0.336s 0:17.34 95.7% 0+0k 0+0io 0pf+0w