Mon Oct 10 17:17:30 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 Mon Oct 10 2011 at 17:17:30 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2814 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: 0.5457444 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): -47.45500 4.413000 ymin,ymax (A): 1.277000 66.50900 zmin,zma (A): -17.15500 29.42200 x,y,z range (A): 51.86800 65.23200 46.57700 scale (grids/A): 0.5457444 object centre (A): -21.52100 33.89300 6.133500 number of atom coordinates read : 2814 total number of charged atoms : 2650 net assigned charge : 4.000022 assigned positive charge : 415.1565 centred at (gu) : 89.63156 88.83282 90.50034 assigned negative charge : -411.1576 centred at (gu) : 89.53231 88.88072 90.46052 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5588 nv = 96 ne = 84 npr = 56212 no. pairs analyzed = 56212 no. exposed pairs = 3707 no. arc points = 27382 no. surface atoms = 1245 nbur = 1569 mkacc time = 8.9999996E-02 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 = 1.568000 m= 203 mr = 2749 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3031 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2759 ## 421 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7197 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8393672E-12 5.4890925E-10 midg,1,midg; midg,igrid,midg 7.1328676E-10 -3.4151206E-11 1,midg,midg; igrid,midg,midg -4.0439024E-10 7.6714501E-10 gauss-seidel spectral radius is 0.9826845 estimated iterations to convergence 63 setup time was (sec) 0.3900000 now iterating at: 17:17:30 rms-change max change #iterations 6.7549482E-02 14.71760 at 10iterations 4.4494802E-03 0.7902544 at 20iterations 2.9591878E-04 5.1416397E-02 at 30iterations 2.0944521E-05 3.7164688E-03 at 40iterations 1.6056098E-06 2.5939941E-04 at 50iterations finished qdiffx linear iterations at : 17:17:33 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 1.6056098E-06 2.5939941E-04 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 17:17:34 3.392u 0.162s 0:04.44 79.9% 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 17:17:34 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2814 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: 1.637233 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): -47.45500 4.413000 ymin,ymax (A): 1.277000 66.50900 zmin,zma (A): -17.15500 29.42200 x,y,z range (A): 51.86800 65.23200 46.57700 scale (grids/A): 1.637233 object centre (A): -21.52100 33.89300 6.133500 number of atom coordinates read : 2814 total number of charged atoms : 2650 net assigned charge : 4.000022 assigned positive charge : 415.1565 centred at (gu) : 88.89371 86.49776 91.49998 assigned negative charge : -411.1576 centred at (gu) : 88.59659 86.64157 91.38161 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 61135 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27382 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18951 mr = 40187 m= 1932 mr = 12878 m= 54 mr = 888 m= 0 mr = 3 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 28116 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 326 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 20283 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) : 0.5457444 object centre at (A) : -21.52100 33.89300 6.133500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.7214026E-05 -2.8538739E-04 midg,1,midg; midg,igrid,midg 2.6809199E-02 6.9270446E-03 1,midg,midg; igrid,midg,midg -9.8030297E-03 9.3072122E-03 gauss-seidel spectral radius is 0.9981815 estimated iterations to convergence 186 setup time was (sec) 0.5100000 now iterating at: 17:17:35 rms-change max change #iterations 3.192515 151.2764 at 10iterations 1.323575 61.97958 at 20iterations 0.5484540 32.74786 at 30iterations 0.2274950 8.713644 at 40iterations 9.4721250E-02 3.503550 at 50iterations 3.9277457E-02 1.534738 at 60iterations 1.6381562E-02 0.5553131 at 70iterations 6.8457387E-03 0.2557447 at 80iterations 2.8414994E-03 0.1027241 at 90iterations 1.1809916E-03 4.7633171E-02 at 100iterations 4.9296330E-04 1.7033100E-02 at 110iterations 2.0445771E-04 8.0642700E-03 at 120iterations finished qdiffx linear iterations at : 17:17:42 total time elapsed so far: 7.530000 # loops : 120 mean,max change (kT/e) : 2.0445771E-04 8.0642700E-03 energy calculations done at 7.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 17:17:43 7.657u 0.213s 0:08.45 93.0% 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 17:17:43 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2814 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: 2.455850 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): -47.45500 4.413000 ymin,ymax (A): 1.277000 66.50900 zmin,zma (A): -17.15500 29.42200 x,y,z range (A): 51.86800 65.23200 46.57700 scale (grids/A): 2.455850 object centre (A): -21.52100 33.89300 6.133500 number of atom coordinates read : 2814 total number of charged atoms : 2650 net assigned charge : 4.000022 assigned positive charge : 415.1565 centred at (gu) : 88.34042 84.74648 92.24973 assigned negative charge : -411.1576 centred at (gu) : 87.89494 84.96237 92.07240 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 141580 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27382 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 65185 mr = 98326 m= 18596 mr = 51102 m= 2871 mr = 13669 m= 167 mr = 1756 m= 3 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7300000 number of dielectric boundary points 63488 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 21178 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) : 1.637233 object centre at (A) : -21.52100 33.89300 6.133500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0239333E-03 -1.4653400E-02 midg,1,midg; midg,igrid,midg 0.4497207 0.2343102 1,midg,midg; igrid,midg,midg -0.1141620 0.1393102 gauss-seidel spectral radius is 0.9991379 estimated iterations to convergence 269 setup time was (sec) 0.9600000 now iterating at: 17:17:44 rms-change max change #iterations 8.354276 392.0726 at 10iterations 4.722381 121.3005 at 20iterations 2.643699 63.72682 at 30iterations 1.471046 37.86612 at 40iterations 0.8167648 20.74607 at 50iterations 0.4509214 9.772491 at 60iterations 0.2491717 5.410961 at 70iterations 0.1372081 3.126122 at 80iterations 7.5725272E-02 1.640106 at 90iterations 4.1583639E-02 0.9970741 at 100iterations 2.2864925E-02 0.5651827 at 110iterations 1.2521378E-02 0.3015404 at 120iterations 6.8984972E-03 0.1379519 at 130iterations 3.7814288E-03 7.8428268E-02 at 140iterations 2.0800270E-03 4.9064636E-02 at 150iterations 1.1437231E-03 2.4989188E-02 at 160iterations 6.2572811E-04 1.2826920E-02 at 170iterations 3.4368018E-04 7.6141357E-03 at 180iterations finished qdiffx linear iterations at : 17:17:55 total time elapsed so far: 12.12000 # loops : 180 mean,max change (kT/e) : 3.4368018E-04 7.6141357E-03 energy calculations done at 12.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.25000 DelPhi exited at 17:17:56 12.255u 0.215s 0:12.88 96.7% 0+0k 0+0io 0pf+0w