Tue Oct 11 03:45:28 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 Tue Oct 11 2011 at 03:45:28 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2715 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6716855 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): -10.38100 37.56900 ymin,ymax (A): -26.61700 21.62800 zmin,zma (A): -7.308000 45.69300 x,y,z range (A): 47.95000 48.24500 53.00100 scale (grids/A): 0.6716855 object centre (A): 13.59400 -2.494499 19.19250 number of atom coordinates read : 2715 total number of charged atoms : 2568 net assigned charge : 4.500017 assigned positive charge : 409.1898 centred at (gu) : 89.89111 90.07037 91.01309 assigned negative charge : -404.6904 centred at (gu) : 89.63873 89.89172 90.98898 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8269 nv = 96 ne = 84 npr = 55273 no. pairs analyzed = 55273 no. exposed pairs = 3237 no. arc points = 22359 no. surface atoms = 1093 nbur = 1622 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 543 mr = 4829 m= 2 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 34 time to turn everything in is 0.3300000 number of dielectric boundary points 3879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2054 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9569 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.4646733E-09 2.7453682E-08 midg,1,midg; midg,igrid,midg -3.4136143E-08 6.5179066E-08 1,midg,midg; igrid,midg,midg -5.7314388E-08 8.1882206E-08 gauss-seidel spectral radius is 0.9885164 estimated iterations to convergence 76 setup time was (sec) 0.5600000 now iterating at: 03:45:29 rms-change max change #iterations 0.1860994 25.38332 at 10iterations 2.0463793E-02 2.592800 at 20iterations 2.3116046E-03 0.2780686 at 30iterations 2.6013935E-04 3.1650543E-02 at 40iterations 3.0962372E-05 4.0950775E-03 at 50iterations finished qdiffx linear iterations at : 03:45:31 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 3.0962372E-05 4.0950775E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 03:45:32 3.465u 0.148s 0:04.03 89.3% 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 Oct 11 2011 at 03:45:32 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 = 2715 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.015056 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): -10.38100 37.56900 ymin,ymax (A): -26.61700 21.62800 zmin,zma (A): -7.308000 45.69300 x,y,z range (A): 47.95000 48.24500 53.00100 scale (grids/A): 2.015056 object centre (A): 13.59400 -2.494499 19.19250 number of atom coordinates read : 2715 total number of charged atoms : 2568 net assigned charge : 4.500017 assigned positive charge : 409.1898 centred at (gu) : 89.67299 90.21050 93.03879 assigned negative charge : -404.6904 centred at (gu) : 88.91594 89.67483 92.96683 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 88483 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22359 grid for indexing accessible points = 1.400000 m= 35896 mr = 63568 m= 6921 mr = 27698 m= 565 mr = 4638 m= 8 mr = 265 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 1882 time to turn everything in is 0.6800000 number of dielectric boundary points 35704 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 105 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 20318 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) : 0.6716855 object centre at (A) : 13.59400 -2.494499 19.19250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4792006E-02 5.0409422E-03 midg,1,midg; midg,igrid,midg -1.1028129E-02 5.3022634E-02 1,midg,midg; igrid,midg,midg -1.3237269E-02 8.0047958E-02 gauss-seidel spectral radius is 0.9987841 estimated iterations to convergence 227 setup time was (sec) 0.9900000 now iterating at: 03:45:33 rms-change max change #iterations 4.837905 197.3157 at 10iterations 2.377960 72.06590 at 20iterations 1.163514 34.10931 at 30iterations 0.5695578 16.34040 at 40iterations 0.2793997 7.879263 at 50iterations 0.1371691 4.140515 at 60iterations 6.7145579E-02 2.051563 at 70iterations 3.2877028E-02 1.089952 at 80iterations 1.6139129E-02 0.4494400 at 90iterations 7.8860102E-03 0.2109566 at 100iterations 3.8751815E-03 0.1083488 at 110iterations 1.8986571E-03 5.4153442E-02 at 120iterations finished qdiffx linear iterations at : 03:45:40 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 1.8986571E-03 5.4153442E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.010000 DelPhi exited at 03:45:41 8.017u 0.219s 0:08.62 95.3% 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 Oct 11 2011 at 03:45:41 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 = 2715 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.022584 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): -10.38100 37.56900 ymin,ymax (A): -26.61700 21.62800 zmin,zma (A): -7.308000 45.69300 x,y,z range (A): 47.95000 48.24500 53.00100 scale (grids/A): 3.022584 object centre (A): 13.59400 -2.494499 19.19250 number of atom coordinates read : 2715 total number of charged atoms : 2568 net assigned charge : 4.500017 assigned positive charge : 409.1898 centred at (gu) : 89.50917 90.31554 94.55796 assigned negative charge : -404.6904 centred at (gu) : 88.37381 89.51212 94.45015 start vw surface at 0.1600000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 203873 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22359 grid for indexing accessible points = 1.400000 m= 111970 mr = 152748 m= 46006 mr = 93860 m= 12831 mr = 38220 m= 2367 mr = 10057 m= 234 mr = 1768 m= 7 mr = 130 m= 0 mr = 0 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 6238 time to turn everything in is 1.770000 number of dielectric boundary points 80505 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 20544 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) : 2.015056 object centre at (A) : 13.59400 -2.494499 19.19250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2889986 0.2461156 midg,1,midg; midg,igrid,midg -0.1289405 0.5555456 1,midg,midg; igrid,midg,midg -5.5883814E-02 0.6793229 gauss-seidel spectral radius is 0.9992938 estimated iterations to convergence 297 setup time was (sec) 2.110000 now iterating at: 03:45:43 rms-change max change #iterations 11.00236 372.6254 at 10iterations 6.508603 157.2613 at 20iterations 3.840023 88.16334 at 30iterations 2.256517 39.30399 at 40iterations 1.325353 24.10271 at 50iterations 0.7774339 13.76681 at 60iterations 0.4559624 9.674844 at 70iterations 0.2667603 4.658813 at 80iterations 0.1560500 2.486893 at 90iterations 9.1202721E-02 1.504673 at 100iterations 5.3248532E-02 0.8839912 at 110iterations 3.1161813E-02 0.5643311 at 120iterations 1.8193074E-02 0.3021994 at 130iterations 1.0644602E-02 0.1902676 at 140iterations 6.2291273E-03 0.1014843 at 150iterations 3.6478606E-03 6.3137054E-02 at 160iterations 2.1459491E-03 3.7002563E-02 at 170iterations 1.2688745E-03 2.1132469E-02 at 180iterations finished qdiffx linear iterations at : 03:45:54 total time elapsed so far: 13.13000 # loops : 180 mean,max change (kT/e) : 1.2688745E-03 2.1132469E-02 energy calculations done at 13.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.36000 DelPhi exited at 03:45:55 13.358u 0.227s 0:14.14 95.9% 0+0k 0+0io 0pf+0w