Wed Dec 21 14:20:24 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 14:20:24 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 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: 0.6033592 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): -10.35400 34.96700 ymin,ymax (A): 0.4080001 41.05800 zmin,zma (A): -30.77100 28.23200 x,y,z range (A): 45.32100 40.65000 59.00300 scale (grids/A): 0.6033592 object centre (A): 12.30650 20.73300 -1.269500 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 3.000002 assigned positive charge : 287.5791 centred at (gu) : 89.55047 89.54144 90.58708 assigned negative charge : -284.5793 centred at (gu) : 89.64327 89.68048 90.61034 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4729 nv = 96 ne = 84 npr = 40836 no. pairs analyzed = 40836 no. exposed pairs = 2488 no. arc points = 17265 no. surface atoms = 848 nbur = 1112 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 208 mr = 2538 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1500000 number of dielectric boundary points 2382 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1746 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 5818 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8396027E-09 8.0685542E-10 midg,1,midg; midg,igrid,midg 6.0689556E-09 -2.5008327E-09 1,midg,midg; igrid,midg,midg 4.5746091E-09 -1.2352516E-09 gauss-seidel spectral radius is 0.9857254 estimated iterations to convergence 69 setup time was (sec) 0.3400000 now iterating at: 14:20:24 rms-change max change #iterations 9.4314344E-02 15.22696 at 10iterations 7.8963786E-03 1.468349 at 20iterations 6.7600101E-04 0.1206584 at 30iterations 5.6832727E-05 9.3460083E-03 at 40iterations 4.8839597E-06 9.4604492E-04 at 50iterations finished qdiffx linear iterations at : 14:20:27 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 4.8839597E-06 9.4604492E-04 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 14:20:28 3.325u 0.171s 0:03.99 87.4% 0+0k 0+0io 6pf+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 14:20:28 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 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: 1.810078 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): -10.35400 34.96700 ymin,ymax (A): 0.4080001 41.05800 zmin,zma (A): -30.77100 28.23200 x,y,z range (A): 45.32100 40.65000 59.00300 scale (grids/A): 1.810078 object centre (A): 12.30650 20.73300 -1.269500 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 3.000002 assigned positive charge : 287.5791 centred at (gu) : 88.65120 88.62444 91.76128 assigned negative charge : -284.5793 centred at (gu) : 88.92989 89.04157 91.83131 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 51362 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17265 grid for indexing accessible points = 1.400000 m= 17182 mr = 35077 m= 2181 mr = 12533 m= 88 mr = 1277 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 21902 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 153 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 14273 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) : 0.6033592 object centre at (A) : 12.30650 20.73300 -1.269500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5393644E-02 2.1006403E-02 midg,1,midg; midg,igrid,midg 4.3873489E-03 -5.1777828E-03 1,midg,midg; igrid,midg,midg -2.4807199E-03 -4.2685312E-03 gauss-seidel spectral radius is 0.9984112 estimated iterations to convergence 199 setup time was (sec) 0.4500000 now iterating at: 14:20:28 rms-change max change #iterations 3.157799 188.7469 at 10iterations 1.397996 58.84654 at 20iterations 0.6171322 25.68729 at 30iterations 0.2707221 10.65033 at 40iterations 0.1194961 4.593477 at 50iterations 5.2541394E-02 2.161369 at 60iterations 2.3149420E-02 0.8950577 at 70iterations 1.0234508E-02 0.3927689 at 80iterations 4.5069084E-03 0.1742392 at 90iterations 1.9839150E-03 7.4529648E-02 at 100iterations 8.7770668E-04 3.2871246E-02 at 110iterations 3.8719503E-04 1.6682625E-02 at 120iterations finished qdiffx linear iterations at : 14:20:35 total time elapsed so far: 7.400000 # loops : 120 mean,max change (kT/e) : 3.8719503E-04 1.6682625E-02 energy calculations done at 7.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.530000 DelPhi exited at 14:20:36 7.528u 0.211s 0:08.01 96.5% 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 14:20:36 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 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: 2.715116 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): -10.35400 34.96700 ymin,ymax (A): 0.4080001 41.05800 zmin,zma (A): -30.77100 28.23200 x,y,z range (A): 45.32100 40.65000 59.00300 scale (grids/A): 2.715116 object centre (A): 12.30650 20.73300 -1.269500 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 3.000002 assigned positive charge : 287.5791 centred at (gu) : 87.97676 87.93671 92.64180 assigned negative charge : -284.5793 centred at (gu) : 88.39488 88.56239 92.74699 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 118788 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17265 grid for indexing accessible points = 1.400000 m= 57223 mr = 84784 m= 18738 mr = 46679 m= 3784 mr = 15135 m= 383 mr = 2657 m= 13 mr = 241 m= 0 mr = 6 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 49427 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 14624 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) : 1.810078 object centre at (A) : 12.30650 20.73300 -1.269500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1897993 0.1352300 midg,1,midg; midg,igrid,midg 1.3344846E-02 -6.9906503E-02 1,midg,midg; igrid,midg,midg -6.5144621E-02 -7.1482018E-02 gauss-seidel spectral radius is 0.9991773 estimated iterations to convergence 275 setup time was (sec) 0.8600000 now iterating at: 14:20:37 rms-change max change #iterations 7.666697 265.9327 at 10iterations 4.315794 130.8682 at 20iterations 2.417111 61.93332 at 30iterations 1.349041 32.55025 at 40iterations 0.7526014 16.32586 at 50iterations 0.4172724 9.106062 at 60iterations 0.2318760 5.014799 at 70iterations 0.1288372 2.827286 at 80iterations 7.1548522E-02 1.523273 at 90iterations 3.9886232E-02 0.8901901 at 100iterations 2.2156928E-02 0.4876709 at 110iterations 1.2333782E-02 0.3079715 at 120iterations 6.8575125E-03 0.1644669 at 130iterations 3.8066807E-03 8.2505703E-02 at 140iterations 2.1139600E-03 4.9091339E-02 at 150iterations 1.1767006E-03 2.6238441E-02 at 160iterations 6.5499701E-04 1.4356613E-02 at 170iterations 3.6331086E-04 7.5912476E-03 at 180iterations finished qdiffx linear iterations at : 14:20:50 total time elapsed so far: 13.56000 # loops : 180 mean,max change (kT/e) : 3.6331086E-04 7.5912476E-03 energy calculations done at 13.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.70000 DelPhi exited at 14:20:50 13.699u 0.234s 0:14.40 96.6% 0+0k 0+0io 0pf+0w