Tue Oct 11 08:33:08 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 08:33:08 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 = 2048 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: 0.7122991 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): -8.035000 35.74000 ymin,ymax (A): -27.53800 16.31800 zmin,zma (A): -4.492000 45.48700 x,y,z range (A): 43.77500 43.85600 49.97900 scale (grids/A): 0.7122991 object centre (A): 13.85250 -5.610000 20.49750 number of atom coordinates read : 2048 total number of charged atoms : 1911 net assigned charge : 4.500009 assigned positive charge : 303.6658 centred at (gu) : 90.38819 89.93816 91.39267 assigned negative charge : -299.1660 centred at (gu) : 90.13393 89.71878 91.36838 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7254 nv = 96 ne = 84 npr = 40879 no. pairs analyzed = 40879 no. exposed pairs = 2617 no. arc points = 18245 no. surface atoms = 883 nbur = 1165 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 525 mr = 4079 m= 2 mr = 86 m= 0 mr = 0 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 3616 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1580 ## 124 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7750 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2782610E-08 7.1604575E-08 midg,1,midg; midg,igrid,midg -7.7083300E-08 1.5342113E-07 1,midg,midg; igrid,midg,midg -8.8122540E-08 1.8647854E-07 gauss-seidel spectral radius is 0.9897289 estimated iterations to convergence 80 setup time was (sec) 0.5400000 now iterating at: 08:33:09 rms-change max change #iterations 0.2013053 29.91330 at 10iterations 2.5344517E-02 3.835205 at 20iterations 3.2121199E-03 0.4011810 at 30iterations 4.2933258E-04 5.5963516E-02 at 40iterations 6.9897971E-05 9.7827911E-03 at 50iterations finished qdiffx linear iterations at : 08:33:11 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 6.9897971E-05 9.7827911E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 08:33:12 3.420u 0.164s 0:04.13 86.6% 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 Oct 11 2011 at 08:33:12 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 = 2048 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.136897 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): -8.035000 35.74000 ymin,ymax (A): -27.53800 16.31800 zmin,zma (A): -4.492000 45.48700 x,y,z range (A): 43.77500 43.85600 49.97900 scale (grids/A): 2.136897 object centre (A): 13.85250 -5.610000 20.49750 number of atom coordinates read : 2048 total number of charged atoms : 1911 net assigned charge : 4.500009 assigned positive charge : 303.6658 centred at (gu) : 91.16431 89.81450 94.17795 assigned negative charge : -299.1660 centred at (gu) : 90.40179 89.15635 94.10509 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 75701 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18245 grid for indexing accessible points = 1.400000 m= 31272 mr = 52552 m= 6588 mr = 23875 m= 586 mr = 4441 m= 12 mr = 268 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 33023 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 58 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 15192 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) : 0.7122991 object centre at (A) : 13.85250 -5.610000 20.49750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4299642E-02 1.5151550E-02 midg,1,midg; midg,igrid,midg -1.1106355E-02 4.1626059E-02 1,midg,midg; igrid,midg,midg -3.4379009E-02 7.4788429E-02 gauss-seidel spectral radius is 0.9988544 estimated iterations to convergence 234 setup time was (sec) 0.8900000 now iterating at: 08:33:13 rms-change max change #iterations 4.607668 166.6055 at 10iterations 2.279301 72.92657 at 20iterations 1.140998 36.56805 at 30iterations 0.5712536 18.75978 at 40iterations 0.2846866 8.212232 at 50iterations 0.1419974 4.037178 at 60iterations 7.0896275E-02 2.197334 at 70iterations 3.5360977E-02 1.247034 at 80iterations 1.7729806E-02 0.4909191 at 90iterations 8.8748336E-03 0.2467194 at 100iterations 4.4353101E-03 0.1457987 at 110iterations 2.2323779E-03 6.5550327E-02 at 120iterations finished qdiffx linear iterations at : 08:33:20 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 2.2323779E-03 6.5550327E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 08:33:21 7.837u 0.182s 0:08.37 95.6% 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 Oct 11 2011 at 08:33:21 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 = 2048 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: 3.205346 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): -8.035000 35.74000 ymin,ymax (A): -27.53800 16.31800 zmin,zma (A): -4.492000 45.48700 x,y,z range (A): 43.77500 43.85600 49.97900 scale (grids/A): 3.205346 object centre (A): 13.85250 -5.610000 20.49750 number of atom coordinates read : 2048 total number of charged atoms : 1911 net assigned charge : 4.500009 assigned positive charge : 303.6658 centred at (gu) : 91.74661 89.72169 96.26697 assigned negative charge : -299.1660 centred at (gu) : 90.60272 88.73453 96.15765 start vw surface at 0.1500000 fill in re-entrant regions at 0.8600000 boundary points on vw surface= 174185 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18245 grid for indexing accessible points = 1.400000 m= 95234 mr = 126512 m= 41196 mr = 79013 m= 12592 mr = 34110 m= 2509 mr = 9894 m= 236 mr = 1820 m= 3 mr = 117 m= 0 mr = 2 time to grow re-entrant surface = 0.9800001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.960000 number of dielectric boundary points 74487 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.090000 number of grid points assigned charge 15288 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) : 2.136897 object centre at (A) : 13.85250 -5.610000 20.49750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2291858 0.3336500 midg,1,midg; midg,igrid,midg -0.1438860 0.2571061 1,midg,midg; igrid,midg,midg -0.3927039 0.5920776 gauss-seidel spectral radius is 0.9993057 estimated iterations to convergence 299 setup time was (sec) 2.260000 now iterating at: 08:33:23 rms-change max change #iterations 10.29743 377.8705 at 10iterations 6.102413 149.7728 at 20iterations 3.619689 76.59323 at 30iterations 2.145868 41.74295 at 40iterations 1.264855 27.75174 at 50iterations 0.7480543 14.10713 at 60iterations 0.4405139 8.477631 at 70iterations 0.2584458 4.554356 at 80iterations 0.1520524 2.725790 at 90iterations 8.9042105E-02 1.597078 at 100iterations 5.2413255E-02 0.9612293 at 110iterations 3.0791219E-02 0.5428047 at 120iterations 1.8110134E-02 0.3321133 at 130iterations 1.0616596E-02 0.1855955 at 140iterations 6.2725777E-03 0.1218166 at 150iterations 3.7142313E-03 6.3095093E-02 at 160iterations 2.2235720E-03 4.1946411E-02 at 170iterations 1.3517687E-03 2.3723602E-02 at 180iterations finished qdiffx linear iterations at : 08:33:34 total time elapsed so far: 13.10000 # loops : 180 mean,max change (kT/e) : 1.3517687E-03 2.3723602E-02 energy calculations done at 13.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.31000 DelPhi exited at 08:33:35 13.315u 0.212s 0:13.83 97.7% 0+0k 0+0io 0pf+0w