Tue Nov 22 14:14:13 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+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 Tue Nov 22 2011 at 14:14:18 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1942 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: 0.6449742 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): -34.67000 10.64300 ymin,ymax (A): 1.399000 41.71500 zmin,zma (A): -0.2900000 54.90600 x,y,z range (A): 45.31300 40.31600 55.19600 scale (grids/A): 0.6449742 object centre (A): -12.01350 21.55700 27.30800 number of atom coordinates read : 1942 total number of charged atoms : 1810 net assigned charge : 3.000004 assigned positive charge : 288.8440 centred at (gu) : 90.10881 89.23002 90.39597 assigned negative charge : -285.8443 centred at (gu) : 90.03532 89.35882 90.37702 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5485 nv = 96 ne = 84 npr = 40116 no. pairs analyzed = 40116 no. exposed pairs = 2404 no. arc points = 16687 no. surface atoms = 814 nbur = 1128 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 273 mr = 3062 m= 2 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 2665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1695 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 6428 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8209302E-09 7.3583641E-09 midg,1,midg; midg,igrid,midg 2.0522375E-08 -6.6685177E-09 1,midg,midg; igrid,midg,midg -2.3034554E-09 1.2364362E-08 gauss-seidel spectral radius is 0.9874849 estimated iterations to convergence 73 setup time was (sec) 0.4300000 now iterating at: 14:14:21 rms-change max change #iterations 0.1325844 21.40360 at 10iterations 1.3076704E-02 1.779442 at 20iterations 1.2957396E-03 0.1984406 at 30iterations 1.2894020E-04 2.0109177E-02 at 40iterations 1.3250890E-05 1.9207001E-03 at 50iterations finished qdiffx linear iterations at : 14:14:29 total time elapsed so far: 2.880000 # loops : 50 mean,max change (kT/e) : 1.3250890E-05 1.9207001E-03 energy calculations done at 2.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.060000 DelPhi exited at 14:14:32 3.060u 0.133s 0:14.92 21.3% 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 Tue Nov 22 2011 at 14:14:34 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1942 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: 1.934923 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): -34.67000 10.64300 ymin,ymax (A): 1.399000 41.71500 zmin,zma (A): -0.2900000 54.90600 x,y,z range (A): 45.31300 40.31600 55.19600 scale (grids/A): 1.934923 object centre (A): -12.01350 21.55700 27.30800 number of atom coordinates read : 1942 total number of charged atoms : 1810 net assigned charge : 3.000004 assigned positive charge : 288.8440 centred at (gu) : 90.32658 87.69025 91.18807 assigned negative charge : -285.8443 centred at (gu) : 90.10603 88.07652 91.13117 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 58480 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16687 grid for indexing accessible points = 1.400000 m= 22459 mr = 40376 m= 3787 mr = 17266 m= 221 mr = 2491 m= 1 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 24744 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 102 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 14267 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) : 0.6449742 object centre at (A) : -12.01350 21.55700 27.30800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1949294E-02 5.3304374E-02 midg,1,midg; midg,igrid,midg 6.9042048E-03 -1.0865729E-02 1,midg,midg; igrid,midg,midg -2.1401686E-03 -4.2626658E-03 gauss-seidel spectral radius is 0.9985982 estimated iterations to convergence 212 setup time was (sec) 0.6700000 now iterating at: 14:14:39 rms-change max change #iterations 3.714494 171.1563 at 10iterations 1.725010 63.42833 at 20iterations 0.8028700 30.53394 at 30iterations 0.3721629 12.76163 at 40iterations 0.1727162 6.162731 at 50iterations 7.9810940E-02 2.818939 at 60iterations 3.6860175E-02 1.346395 at 70iterations 1.7143136E-02 0.6157022 at 80iterations 7.9515027E-03 0.2700233 at 90iterations 3.6849780E-03 0.1297865 at 100iterations 1.7088703E-03 6.0668945E-02 at 110iterations 7.9184590E-04 2.8047144E-02 at 120iterations finished qdiffx linear iterations at : 14:14:57 total time elapsed so far: 6.670000 # loops : 120 mean,max change (kT/e) : 7.9184590E-04 2.8047144E-02 energy calculations done at 6.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.850000 DelPhi exited at 14:15:00 6.849u 0.168s 0:26.26 26.6% 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 Tue Nov 22 2011 at 14:15:01 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1942 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: 2.902384 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): -34.67000 10.64300 ymin,ymax (A): 1.399000 41.71500 zmin,zma (A): -0.2900000 54.90600 x,y,z range (A): 45.31300 40.31600 55.19600 scale (grids/A): 2.902384 object centre (A): -12.01350 21.55700 27.30800 number of atom coordinates read : 1942 total number of charged atoms : 1810 net assigned charge : 3.000004 assigned positive charge : 288.8440 centred at (gu) : 90.48987 86.53532 91.78217 assigned negative charge : -285.8443 centred at (gu) : 90.15911 87.11487 91.69695 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 134832 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16687 grid for indexing accessible points = 1.400000 m= 70968 mr = 97363 m= 27895 mr = 59190 m= 6908 mr = 23279 m= 922 mr = 5348 m= 55 mr = 589 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.040000 number of dielectric boundary points 55780 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 14480 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) : 1.934923 object centre at (A) : -12.01350 21.55700 27.30800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.6955566E-02 0.4118725 midg,1,midg; midg,igrid,midg 1.4652947E-02 -0.1319837 1,midg,midg; igrid,midg,midg -7.0649251E-02 -7.9826124E-02 gauss-seidel spectral radius is 0.9992321 estimated iterations to convergence 285 setup time was (sec) 1.320000 now iterating at: 14:15:09 rms-change max change #iterations 8.685718 364.2600 at 10iterations 4.989495 120.0009 at 20iterations 2.845237 58.52010 at 30iterations 1.623199 40.23958 at 40iterations 0.9248736 17.76160 at 50iterations 0.5254657 10.25792 at 60iterations 0.2986991 5.893188 at 70iterations 0.1699065 3.310974 at 80iterations 9.6347973E-02 1.963797 at 90iterations 5.4785971E-02 1.131916 at 100iterations 3.1091310E-02 0.6146393 at 110iterations 1.7649727E-02 0.3756828 at 120iterations 1.0000747E-02 0.1885910 at 130iterations 5.6910408E-03 0.1143799 at 140iterations 3.2290451E-03 6.5811157E-02 at 150iterations 1.8335066E-03 3.8318634E-02 at 160iterations 1.0439855E-03 2.0276070E-02 at 170iterations 5.9442397E-04 1.2740612E-02 at 180iterations finished qdiffx linear iterations at : 14:15:39 total time elapsed so far: 11.26000 # loops : 180 mean,max change (kT/e) : 5.9442397E-04 1.2740612E-02 energy calculations done at 11.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.44000 DelPhi exited at 14:15:41 11.445u 0.169s 0:39.55 29.3% 0+0k 0+0io 0pf+0w