Mon Oct 10 18:52:05 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 18:52:05 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4248 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: 0.5209248 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): 21.42000 75.37200 ymin,ymax (A): 27.01000 95.35000 zmin,zma (A): 147.5060 209.5780 x,y,z range (A): 53.95200 68.34000 62.07201 scale (grids/A): 0.5209248 object centre (A): 48.39600 61.18000 178.5420 number of atom coordinates read : 4248 total number of charged atoms : 4097 net assigned charge : 1.500036 assigned positive charge : 654.4253 centred at (gu) : 90.02338 90.11595 86.84137 assigned negative charge : -652.9290 centred at (gu) : 89.91296 90.13342 86.90847 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7415 nv = 96 ne = 84 npr = 83817 no. pairs analyzed = 83817 no. exposed pairs = 5615 no. arc points = 39145 no. surface atoms = 1872 nbur = 2376 mkacc time = 0.1500000 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 = 1.652000 m= 282 mr = 3759 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3933 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3860 ## 579 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 9938 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.1392097E-10 -9.6706781E-11 midg,1,midg; midg,igrid,midg 8.4950449E-11 -3.9734042E-11 1,midg,midg; igrid,midg,midg -3.7725709E-10 4.1991566E-10 gauss-seidel spectral radius is 0.9811167 estimated iterations to convergence 60 setup time was (sec) 0.4800000 now iterating at: 18:52:06 rms-change max change #iterations 6.9039226E-02 11.77893 at 10iterations 4.9219970E-03 0.7614174 at 20iterations 8.7279006E-04 0.1587372 at 30iterations 2.8713638E-04 5.7350159E-02 at 40iterations 1.1547076E-04 2.2926331E-02 at 50iterations finished qdiffx linear iterations at : 18:52:09 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 1.1547076E-04 2.2926331E-02 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 18:52:09 3.549u 0.195s 0:04.05 92.0% 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 18:52:09 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4248 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: 1.562774 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): 21.42000 75.37200 ymin,ymax (A): 27.01000 95.35000 zmin,zma (A): 147.5060 209.5780 x,y,z range (A): 53.95200 68.34000 62.07201 scale (grids/A): 1.562774 object centre (A): 48.39600 61.18000 178.5420 number of atom coordinates read : 4248 total number of charged atoms : 4097 net assigned charge : 1.500036 assigned positive charge : 654.4253 centred at (gu) : 90.06866 90.34658 80.52266 assigned negative charge : -652.9290 centred at (gu) : 89.73856 90.40015 80.72518 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 83020 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39145 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 25095 mr = 56242 m= 2441 mr = 16603 m= 62 mr = 1036 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 52 time to turn everything in is 0.4000000 number of dielectric boundary points 36737 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 535 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 30954 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) : 0.5209248 object centre at (A) : 48.39600 61.18000 178.5420 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4815081E-03 -6.2931427E-03 midg,1,midg; midg,igrid,midg 1.5676972E-02 1.5682576E-02 1,midg,midg; igrid,midg,midg -2.8094510E-03 2.1154983E-03 gauss-seidel spectral radius is 0.9981410 estimated iterations to convergence 184 setup time was (sec) 0.6200000 now iterating at: 18:52:10 rms-change max change #iterations 3.793418 182.7129 at 10iterations 1.566459 55.45480 at 20iterations 0.6445700 21.43192 at 30iterations 0.2671896 9.325268 at 40iterations 0.1102424 3.756123 at 50iterations 4.5623783E-02 1.447331 at 60iterations 1.9023836E-02 0.6035004 at 70iterations 7.9625752E-03 0.3138428 at 80iterations 3.4412881E-03 0.1214294 at 90iterations 1.5978232E-03 5.9669495E-02 at 100iterations 8.5668470E-04 3.4473419E-02 at 110iterations 5.4004736E-04 2.4757385E-02 at 120iterations finished qdiffx linear iterations at : 18:52:18 total time elapsed so far: 7.900000 # loops : 120 mean,max change (kT/e) : 5.4004736E-04 2.4757385E-02 energy calculations done at 7.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.030000 DelPhi exited at 18:52:18 8.036u 0.240s 0:08.77 94.2% 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 18:52:18 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4248 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: 2.344162 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): 21.42000 75.37200 ymin,ymax (A): 27.01000 95.35000 zmin,zma (A): 147.5060 209.5780 x,y,z range (A): 53.95200 68.34000 62.07201 scale (grids/A): 2.344162 object centre (A): 48.39600 61.18000 178.5420 number of atom coordinates read : 4248 total number of charged atoms : 4097 net assigned charge : 1.500036 assigned positive charge : 654.4253 centred at (gu) : 90.10269 90.51982 75.78371 assigned negative charge : -652.9290 centred at (gu) : 89.60768 90.60012 76.08776 start vw surface at 0.1200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 193307 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39145 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 88273 mr = 138402 m= 23627 mr = 68351 m= 3588 mr = 16998 m= 193 mr = 2161 m= 2 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 131 time to turn everything in is 1.000000 number of dielectric boundary points 83030 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 56 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 32697 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) : 1.562774 object centre at (A) : 48.39600 61.18000 178.5420 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1010780 -0.1039743 midg,1,midg; midg,igrid,midg 0.2968289 0.4678823 1,midg,midg; igrid,midg,midg -1.7582115E-02 3.4187663E-02 gauss-seidel spectral radius is 0.9991571 estimated iterations to convergence 272 setup time was (sec) 1.260000 now iterating at: 18:52:20 rms-change max change #iterations 10.24074 326.3631 at 10iterations 5.904359 138.9325 at 20iterations 3.369582 82.54303 at 30iterations 1.911054 42.29462 at 40iterations 1.078406 25.70915 at 50iterations 0.6051685 12.17863 at 60iterations 0.3386026 6.812595 at 70iterations 0.1892409 3.653271 at 80iterations 0.1056375 2.372360 at 90iterations 5.8854256E-02 1.097267 at 100iterations 3.2812029E-02 0.5990346 at 110iterations 1.8264057E-02 0.3614826 at 120iterations 1.0180620E-02 0.2189741 at 130iterations 5.6651933E-03 0.1035557 at 140iterations 3.1700800E-03 6.2080383E-02 at 150iterations 1.7790716E-03 3.4149170E-02 at 160iterations 1.0141061E-03 2.3780584E-02 at 170iterations 5.9150724E-04 1.2706757E-02 at 180iterations finished qdiffx linear iterations at : 18:52:32 total time elapsed so far: 13.15000 # loops : 180 mean,max change (kT/e) : 5.9150724E-04 1.2706757E-02 energy calculations done at 13.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.29000 DelPhi exited at 18:52:32 13.287u 0.221s 0:14.04 96.1% 0+0k 0+0io 0pf+0w