Sun Oct 9 13:13:06 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 Sun Oct 9 2011 at 13:13:06 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2352 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 0.7069804 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): -18.80800 30.23900 ymin,ymax (A): -20.43700 29.91800 zmin,zma (A): 4.502000 48.94000 x,y,z range (A): 49.04700 50.35500 44.43800 scale (grids/A): 0.7069804 object centre (A): 5.715500 4.740500 26.72100 number of atom coordinates read : 2352 total number of charged atoms : 2207 net assigned charge : 2.406013 assigned positive charge : 357.4752 centred at (gu) : 90.80241 90.21219 90.02871 assigned negative charge : -355.0696 centred at (gu) : 90.90401 90.38157 90.12600 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8104 nv = 96 ne = 84 npr = 47040 no. pairs analyzed = 47040 no. exposed pairs = 3049 no. arc points = 21041 no. surface atoms = 1020 nbur = 1332 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 539 mr = 4547 m= 2 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 4005 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1865 ## 175 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8822 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.4192819E-08 -3.3921221E-08 midg,1,midg; midg,igrid,midg 1.0903030E-07 -7.8246501E-08 1,midg,midg; igrid,midg,midg 6.5779680E-08 -4.2727905E-08 gauss-seidel spectral radius is 0.9896026 estimated iterations to convergence 80 setup time was (sec) 0.3800000 now iterating at: 13:13:07 rms-change max change #iterations 0.2186717 29.66282 at 10iterations 2.7073279E-02 3.430862 at 20iterations 4.0769107E-03 0.5697517 at 30iterations 9.3122339E-04 0.1486969 at 40iterations 3.0416861E-04 4.6394348E-02 at 50iterations finished qdiffx linear iterations at : 13:13:09 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 3.0416861E-04 4.6394348E-02 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 13:13:10 3.388u 0.176s 0:03.85 92.2% 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 Sun Oct 9 2011 at 13:13:10 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2352 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 2.120941 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): -18.80800 30.23900 ymin,ymax (A): -20.43700 29.91800 zmin,zma (A): 4.502000 48.94000 x,y,z range (A): 49.04700 50.35500 44.43800 scale (grids/A): 2.120941 object centre (A): 5.715500 4.740500 26.72100 number of atom coordinates read : 2352 total number of charged atoms : 2207 net assigned charge : 2.406013 assigned positive charge : 357.4752 centred at (gu) : 92.40704 90.63633 90.08569 assigned negative charge : -355.0696 centred at (gu) : 92.71194 91.14450 90.37768 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 85921 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21041 grid for indexing accessible points = 1.400000 m= 33522 mr = 60154 m= 6229 mr = 24905 m= 621 mr = 4109 m= 16 mr = 313 m= 0 mr = 1 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 36827 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 82 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 17508 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) : 0.7069804 object centre at (A) : 5.715500 4.740500 26.72100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2351685E-02 8.0097653E-03 midg,1,midg; midg,igrid,midg -1.4649324E-02 -0.1175557 1,midg,midg; igrid,midg,midg -2.0877018E-03 -3.9543281E-03 gauss-seidel spectral radius is 0.9988654 estimated iterations to convergence 235 setup time was (sec) 0.6500000 now iterating at: 13:13:11 rms-change max change #iterations 4.980389 201.6850 at 10iterations 2.488304 74.15660 at 20iterations 1.245290 35.80753 at 30iterations 0.6231172 18.09198 at 40iterations 0.3126308 9.784640 at 50iterations 0.1568111 4.484451 at 60iterations 7.8744009E-02 2.202080 at 70iterations 3.9669041E-02 1.090025 at 80iterations 2.0091088E-02 0.6168542 at 90iterations 1.0290195E-02 0.2776566 at 100iterations 5.3587016E-03 0.1651535 at 110iterations 2.8985883E-03 9.4551086E-02 at 120iterations finished qdiffx linear iterations at : 13:13:18 total time elapsed so far: 7.790000 # loops : 120 mean,max change (kT/e) : 2.8985883E-03 9.4551086E-02 energy calculations done at 7.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 13:13:18 7.932u 0.194s 0:08.40 96.6% 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 Sun Oct 9 2011 at 13:13:18 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2352 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 3.181412 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): -18.80800 30.23900 ymin,ymax (A): -20.43700 29.91800 zmin,zma (A): 4.502000 48.94000 x,y,z range (A): 49.04700 50.35500 44.43800 scale (grids/A): 3.181412 object centre (A): 5.715500 4.740500 26.72100 number of atom coordinates read : 2352 total number of charged atoms : 2207 net assigned charge : 2.406013 assigned positive charge : 357.4752 centred at (gu) : 93.61060 90.95442 90.12840 assigned negative charge : -355.0696 centred at (gu) : 94.06779 91.71674 90.56649 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 198106 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21041 grid for indexing accessible points = 1.400000 m= 105076 mr = 144973 m= 41152 mr = 86337 m= 11715 mr = 33492 m= 2488 mr = 9022 m= 269 mr = 1772 m= 12 mr = 169 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.310000 number of dielectric boundary points 83053 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 17655 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) : 2.120941 object centre at (A) : 5.715500 4.740500 26.72100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5968542 -2.4296220E-02 midg,1,midg; midg,igrid,midg -0.5240589 -1.322798 1,midg,midg; igrid,midg,midg -0.1079531 -6.3372910E-02 gauss-seidel spectral radius is 0.9993091 estimated iterations to convergence 300 setup time was (sec) 1.550000 now iterating at: 13:13:20 rms-change max change #iterations 11.15512 397.8257 at 10iterations 6.688723 127.6769 at 20iterations 3.987826 77.18005 at 30iterations 2.378552 45.46968 at 40iterations 1.409868 26.86883 at 50iterations 0.8345273 14.37011 at 60iterations 0.4938282 9.765614 at 70iterations 0.2919914 4.673973 at 80iterations 0.1726113 2.933303 at 90iterations 0.1017247 1.810773 at 100iterations 6.0221370E-02 1.074282 at 110iterations 3.5677522E-02 0.7073319 at 120iterations 2.1432372E-02 0.3924885 at 130iterations 1.3067428E-02 0.2230415 at 140iterations 8.2323346E-03 0.1561356 at 150iterations 5.4275231E-03 0.1139183 at 160iterations 3.8098309E-03 7.9666138E-02 at 170iterations 2.8508054E-03 5.8494568E-02 at 180iterations finished qdiffx linear iterations at : 13:13:32 total time elapsed so far: 13.04000 # loops : 180 mean,max change (kT/e) : 2.8508054E-03 5.8494568E-02 energy calculations done at 13.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.19000 DelPhi exited at 13:13:32 13.187u 0.209s 0:13.66 97.9% 0+0k 0+0io 0pf+0w