Tue Oct 11 06:18:25 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 06:18:25 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2072 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: 0.7049226 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): -20.72000 29.78200 ymin,ymax (A): -11.82100 30.66700 zmin,zma (A): -8.559000 38.39100 x,y,z range (A): 50.50200 42.48800 46.95000 scale (grids/A): 0.7049226 object centre (A): 4.531000 9.423000 14.91600 number of atom coordinates read : 2072 total number of charged atoms : 1944 net assigned charge : 6.500009 assigned positive charge : 314.9560 centred at (gu) : 91.14597 89.81998 90.83639 assigned negative charge : -308.4562 centred at (gu) : 91.09406 89.74477 90.72688 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7020 nv = 96 ne = 84 npr = 41471 no. pairs analyzed = 41471 no. exposed pairs = 2494 no. arc points = 17169 no. surface atoms = 839 nbur = 1233 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 484 mr = 4096 m= 2 mr = 107 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3303 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1588 ## 136 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 7811 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8281710E-10 1.1878568E-07 midg,1,midg; midg,igrid,midg 1.6411159E-08 8.2437232E-08 1,midg,midg; igrid,midg,midg 2.1917185E-08 9.3292471E-08 gauss-seidel spectral radius is 0.9895092 estimated iterations to convergence 79 setup time was (sec) 0.5200000 now iterating at: 06:18:26 rms-change max change #iterations 0.1912895 23.76955 at 10iterations 2.3724539E-02 3.311981 at 20iterations 3.1244953E-03 0.4191284 at 30iterations 4.9405306E-04 6.0957909E-02 at 40iterations 1.1954227E-04 1.5544891E-02 at 50iterations finished qdiffx linear iterations at : 06:18:30 total time elapsed so far: 4.200000 # loops : 50 mean,max change (kT/e) : 1.1954227E-04 1.5544891E-02 energy calculations done at 4.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.370000 DelPhi exited at 06:18:31 4.373u 0.388s 0:05.42 87.6% 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 Tue Oct 11 2011 at 06:18:31 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 = 2072 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: 2.114768 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): -20.72000 29.78200 ymin,ymax (A): -11.82100 30.66700 zmin,zma (A): -8.559000 38.39100 x,y,z range (A): 50.50200 42.48800 46.95000 scale (grids/A): 2.114768 object centre (A): 4.531000 9.423000 14.91600 number of atom coordinates read : 2072 total number of charged atoms : 1944 net assigned charge : 6.500009 assigned positive charge : 314.9560 centred at (gu) : 93.43807 89.45981 92.50935 assigned negative charge : -308.4562 centred at (gu) : 93.28238 89.23438 92.18083 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 74572 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17169 grid for indexing accessible points = 1.400000 m= 30280 mr = 53356 m= 5772 mr = 23232 m= 454 mr = 3851 m= 4 mr = 250 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 30393 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 69 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 15437 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) : 0.7049226 object centre at (A) : 4.531000 9.423000 14.91600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0436629E-02 3.6891311E-02 midg,1,midg; midg,igrid,midg 2.0926610E-02 2.3710983E-02 1,midg,midg; igrid,midg,midg 4.5458645E-02 3.0781826E-02 gauss-seidel spectral radius is 0.9988211 estimated iterations to convergence 231 setup time was (sec) 0.9200000 now iterating at: 06:18:32 rms-change max change #iterations 4.533119 200.0108 at 10iterations 2.235931 79.98233 at 20iterations 1.106114 31.97474 at 30iterations 0.5473301 17.84164 at 40iterations 0.2712520 7.960202 at 50iterations 0.1341595 3.894879 at 60iterations 6.6457964E-02 1.984596 at 70iterations 3.2945063E-02 1.034847 at 80iterations 1.6341003E-02 0.4953575 at 90iterations 8.1929024E-03 0.2687607 at 100iterations 4.0926198E-03 0.1163855 at 110iterations 2.0837942E-03 6.5307617E-02 at 120iterations finished qdiffx linear iterations at : 06:18:41 total time elapsed so far: 10.30000 # loops : 120 mean,max change (kT/e) : 2.0837942E-03 6.5307617E-02 energy calculations done at 10.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.47000 DelPhi exited at 06:18:42 10.475u 0.430s 0:11.18 97.4% 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 06:18:42 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 = 2072 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: 3.172152 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): -20.72000 29.78200 ymin,ymax (A): -11.82100 30.66700 zmin,zma (A): -8.559000 38.39100 x,y,z range (A): 50.50200 42.48800 46.95000 scale (grids/A): 3.172152 object centre (A): 4.531000 9.423000 14.91600 number of atom coordinates read : 2072 total number of charged atoms : 1944 net assigned charge : 6.500009 assigned positive charge : 314.9560 centred at (gu) : 95.15691 89.18983 93.76408 assigned negative charge : -308.4562 centred at (gu) : 94.92368 88.85157 93.27127 start vw surface at 0.1000000 fill in re-entrant regions at 1.090000 boundary points on vw surface= 171905 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17169 grid for indexing accessible points = 1.400000 m= 94143 mr = 128332 m= 38540 mr = 78763 m= 10770 mr = 31964 m= 2000 mr = 8446 m= 222 mr = 1421 m= 6 mr = 133 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.300000 number of dielectric boundary points 68527 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.430000 number of grid points assigned charge 15552 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) : 2.114768 object centre at (A) : 4.531000 9.423000 14.91600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4872153 0.2677177 midg,1,midg; midg,igrid,midg 0.1579872 0.1456003 1,midg,midg; igrid,midg,midg 0.3798168 0.1508159 gauss-seidel spectral radius is 0.9992934 estimated iterations to convergence 297 setup time was (sec) 2.630000 now iterating at: 06:18:45 rms-change max change #iterations 10.17018 351.1949 at 10iterations 5.995492 118.8456 at 20iterations 3.551812 72.93994 at 30iterations 2.087853 40.45176 at 40iterations 1.228428 22.87175 at 50iterations 0.7224017 14.00265 at 60iterations 0.4239296 8.694058 at 70iterations 0.2482669 4.715866 at 80iterations 0.1454169 2.685942 at 90iterations 8.5401230E-02 1.582599 at 100iterations 5.0149221E-02 0.9281359 at 110iterations 2.9492168E-02 0.5569277 at 120iterations 1.7508807E-02 0.3219872 at 130iterations 1.0546112E-02 0.2047234 at 140iterations 6.4975042E-03 0.1190205 at 150iterations 4.1525024E-03 7.9502106E-02 at 160iterations 2.8029848E-03 5.0678253E-02 at 170iterations 2.0112998E-03 3.7378311E-02 at 180iterations finished qdiffx linear iterations at : 06:19:01 total time elapsed so far: 18.47000 # loops : 180 mean,max change (kT/e) : 2.0112998E-03 3.7378311E-02 energy calculations done at 18.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.64000 DelPhi exited at 06:19:01 18.644u 0.436s 0:19.62 97.1% 0+0k 0+0io 0pf+0w