Wed Dec 21 14:21:01 PST 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 Wed Dec 21 2011 at 14:21:01 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 = 1968 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6397585 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): 25.48400 65.44800 ymin,ymax (A): -27.82300 27.82300 zmin,zma (A): 63.02500 103.5500 x,y,z range (A): 39.96400 55.64600 40.52500 scale (grids/A): 0.6397585 object centre (A): 45.46600 0.0000000E+00 83.28751 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 2.000005 assigned positive charge : 287.8180 centred at (gu) : 90.12029 89.99368 90.00521 assigned negative charge : -285.8182 centred at (gu) : 90.32918 89.99726 90.00200 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5526 nv = 96 ne = 84 npr = 40135 no. pairs analyzed = 40135 no. exposed pairs = 2430 no. arc points = 16902 no. surface atoms = 821 nbur = 1147 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 320 mr = 3131 m= 0 mr = 35 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.1700000 number of dielectric boundary points 2680 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1744 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 6477 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6604330E-09 3.2153882E-09 midg,1,midg; midg,igrid,midg 3.2482501E-09 2.6277562E-09 1,midg,midg; igrid,midg,midg 1.9851734E-08 -1.5726730E-08 gauss-seidel spectral radius is 0.9872867 estimated iterations to convergence 73 setup time was (sec) 0.4500000 now iterating at: 14:21:02 rms-change max change #iterations 0.1295158 22.19943 at 10iterations 1.2493636E-02 1.806935 at 20iterations 1.2462054E-03 0.1726465 at 30iterations 1.2372459E-04 2.2036076E-02 at 40iterations 1.1684726E-05 2.2315979E-03 at 50iterations finished qdiffx linear iterations at : 14:21:06 total time elapsed so far: 4.620000 # loops : 50 mean,max change (kT/e) : 1.1684726E-05 2.2315979E-03 energy calculations done at 4.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.760000 DelPhi exited at 14:21:07 4.760u 0.300s 0:05.60 90.3% 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 Wed Dec 21 2011 at 14:21:07 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 = 1968 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: 1.919275 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): 25.48400 65.44800 ymin,ymax (A): -27.82300 27.82300 zmin,zma (A): 63.02500 103.5500 x,y,z range (A): 39.96400 55.64600 40.52500 scale (grids/A): 1.919275 object centre (A): 45.46600 0.0000000E+00 83.28751 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 2.000005 assigned positive charge : 287.8180 centred at (gu) : 90.36083 89.98100 90.01532 assigned negative charge : -285.8182 centred at (gu) : 90.98763 89.99206 90.00631 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 59157 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16902 grid for indexing accessible points = 1.400000 m= 23203 mr = 41117 m= 3843 mr = 17994 m= 163 mr = 2561 m= 2 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 250 time to turn everything in is 0.3600000 number of dielectric boundary points 24644 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 123 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 14488 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) : 0.6397585 object centre at (A) : 45.46600 0.0000000E+00 83.28751 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7046103E-03 3.5604360E-03 midg,1,midg; midg,igrid,midg 4.1571412E-02 4.1321792E-02 1,midg,midg; igrid,midg,midg 8.4143598E-03 -2.7231138E-02 gauss-seidel spectral radius is 0.9985815 estimated iterations to convergence 210 setup time was (sec) 0.6700000 now iterating at: 14:21:09 rms-change max change #iterations 3.657536 159.1553 at 10iterations 1.689178 62.99092 at 20iterations 0.7801527 27.86723 at 30iterations 0.3599169 12.60826 at 40iterations 0.1661558 5.440845 at 50iterations 7.6728001E-02 2.583086 at 60iterations 3.5389833E-02 1.197067 at 70iterations 1.6244741E-02 0.6065674 at 80iterations 7.5302869E-03 0.2520399 at 90iterations 3.4604166E-03 0.1241379 at 100iterations 1.6044807E-03 5.7569504E-02 at 110iterations 7.3838129E-04 2.4694443E-02 at 120iterations finished qdiffx linear iterations at : 14:21:19 total time elapsed so far: 10.97000 # loops : 120 mean,max change (kT/e) : 7.3838129E-04 2.4694443E-02 energy calculations done at 10.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.09000 DelPhi exited at 14:21:26 11.096u 0.426s 0:18.92 60.8% 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 Wed Dec 21 2011 at 14:21:26 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 = 1968 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.878913 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): 25.48400 65.44800 ymin,ymax (A): -27.82300 27.82300 zmin,zma (A): 63.02500 103.5500 x,y,z range (A): 39.96400 55.64600 40.52500 scale (grids/A): 2.878913 object centre (A): 45.46600 0.0000000E+00 83.28751 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 2.000005 assigned positive charge : 287.8180 centred at (gu) : 90.54120 89.97152 90.02291 assigned negative charge : -285.8182 centred at (gu) : 91.48152 89.98807 90.00947 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 136492 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16902 grid for indexing accessible points = 1.400000 m= 71983 mr = 98823 m= 29265 mr = 60503 m= 6893 mr = 24797 m= 745 mr = 5265 m= 32 mr = 440 m= 0 mr = 8 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 879 time to turn everything in is 0.8900000 number of dielectric boundary points 55574 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 14688 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) : 1.919275 object centre at (A) : 45.46600 0.0000000E+00 83.28751 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4195040E-02 2.3485726E-02 midg,1,midg; midg,igrid,midg 0.3325154 0.3298659 1,midg,midg; igrid,midg,midg 2.3455482E-02 -0.3038839 gauss-seidel spectral radius is 0.9992322 estimated iterations to convergence 285 setup time was (sec) 1.290000 now iterating at: 14:21:28 rms-change max change #iterations 8.593900 377.0297 at 10iterations 4.974240 132.2812 at 20iterations 2.841855 74.93460 at 30iterations 1.625756 42.37769 at 40iterations 0.9301120 28.43472 at 50iterations 0.5293356 10.70951 at 60iterations 0.3026059 6.492239 at 70iterations 0.1718368 3.695999 at 80iterations 9.7401507E-02 2.084352 at 90iterations 5.5518534E-02 1.082049 at 100iterations 3.1515349E-02 0.6635768 at 110iterations 1.7866477E-02 0.3928795 at 120iterations 1.0153882E-02 0.2188301 at 130iterations 5.7783010E-03 0.1214790 at 140iterations 3.2913454E-03 7.0514679E-02 at 150iterations 1.8618993E-03 3.6903381E-02 at 160iterations 1.0558799E-03 2.1319866E-02 at 170iterations 6.0088176E-04 1.3530850E-02 at 180iterations finished qdiffx linear iterations at : 14:21:45 total time elapsed so far: 17.57000 # loops : 180 mean,max change (kT/e) : 6.0088176E-04 1.3530850E-02 energy calculations done at 17.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.70000 DelPhi exited at 14:21:53 17.705u 0.367s 0:27.04 66.7% 0+0k 0+0io 0pf+0w