Sun Oct 9 12:13:17 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 Sun Oct 9 2011 at 12:13:17 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 = 2433 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: 0.6959513 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): -13.73100 37.42200 ymin,ymax (A): -1.071000 44.73700 zmin,zma (A): -6.187000 43.07700 x,y,z range (A): 51.15300 45.80800 49.26400 scale (grids/A): 0.6959513 object centre (A): 11.84550 21.83300 18.44500 number of atom coordinates read : 2433 total number of charged atoms : 2291 net assigned charge : 4.500025 assigned positive charge : 373.0550 centred at (gu) : 91.12144 91.41023 89.71332 assigned negative charge : -368.5555 centred at (gu) : 91.28375 91.48279 89.66055 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7706 nv = 96 ne = 84 npr = 49386 no. pairs analyzed = 49386 no. exposed pairs = 3002 no. arc points = 20870 no. surface atoms = 1012 nbur = 1421 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 513 mr = 4237 m= 3 mr = 74 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 0.2000000 number of dielectric boundary points 3911 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1966 ## 179 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8945 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.8138073E-09 5.0903946E-08 midg,1,midg; midg,igrid,midg 4.7524878E-08 -3.9368886E-09 1,midg,midg; igrid,midg,midg 8.1634738E-08 -5.5414727E-08 gauss-seidel spectral radius is 0.9892733 estimated iterations to convergence 79 setup time was (sec) 0.3900000 now iterating at: 12:13:17 rms-change max change #iterations 0.2038570 36.60745 at 10iterations 2.3854939E-02 3.453200 at 20iterations 2.9247012E-03 0.4207363 at 30iterations 3.7927509E-04 4.9486160E-02 at 40iterations 6.9422844E-05 1.1920929E-02 at 50iterations finished qdiffx linear iterations at : 12:13:20 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 6.9422844E-05 1.1920929E-02 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 12:13:21 3.417u 0.164s 0:03.93 90.8% 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 12:13:21 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 = 2433 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: 2.087854 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): -13.73100 37.42200 ymin,ymax (A): -1.071000 44.73700 zmin,zma (A): -6.187000 43.07700 x,y,z range (A): 51.15300 45.80800 49.26400 scale (grids/A): 2.087854 object centre (A): 11.84550 21.83300 18.44500 number of atom coordinates read : 2433 total number of charged atoms : 2291 net assigned charge : 4.500025 assigned positive charge : 373.0550 centred at (gu) : 93.36400 94.23029 89.13924 assigned negative charge : -368.5555 centred at (gu) : 93.85104 94.44794 88.98138 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 80839 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20870 grid for indexing accessible points = 1.400000 m= 31878 mr = 55749 m= 6769 mr = 23818 m= 627 mr = 4477 m= 21 mr = 263 m= 0 mr = 1 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.4200000 number of dielectric boundary points 35826 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 102 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 18182 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) : 0.6959513 object centre at (A) : 11.84550 21.83300 18.44500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7093053E-02 1.9610755E-02 midg,1,midg; midg,igrid,midg 3.9354749E-02 7.7727628E-03 1,midg,midg; igrid,midg,midg 3.0966690E-02 -4.1836478E-02 gauss-seidel spectral radius is 0.9988325 estimated iterations to convergence 232 setup time was (sec) 0.6500000 now iterating at: 12:13:21 rms-change max change #iterations 4.920378 202.5492 at 10iterations 2.421261 89.67982 at 20iterations 1.199720 37.12019 at 30iterations 0.5951604 19.37879 at 40iterations 0.2940534 8.523975 at 50iterations 0.1461676 4.335117 at 60iterations 7.2398394E-02 2.185573 at 70iterations 3.5992209E-02 1.107419 at 80iterations 1.7849203E-02 0.5398626 at 90iterations 8.8594109E-03 0.2603073 at 100iterations 4.4178916E-03 0.1310987 at 110iterations 2.2069688E-03 5.9480667E-02 at 120iterations finished qdiffx linear iterations at : 12:13:29 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 2.2069688E-03 5.9480667E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 12:13:29 7.876u 0.200s 0:08.35 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 12:13:29 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 = 2433 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: 3.131781 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): -13.73100 37.42200 ymin,ymax (A): -1.071000 44.73700 zmin,zma (A): -6.187000 43.07700 x,y,z range (A): 51.15300 45.80800 49.26400 scale (grids/A): 3.131781 object centre (A): 11.84550 21.83300 18.44500 number of atom coordinates read : 2433 total number of charged atoms : 2291 net assigned charge : 4.500025 assigned positive charge : 373.0550 centred at (gu) : 95.04566 96.34511 88.70885 assigned negative charge : -368.5555 centred at (gu) : 95.77660 96.67190 88.47215 start vw surface at 0.1000000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 186488 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20870 grid for indexing accessible points = 1.400000 m= 98163 mr = 134888 m= 41387 mr = 80363 m= 13032 mr = 33921 m= 2616 mr = 10044 m= 262 mr = 1776 m= 14 mr = 121 m= 0 mr = 5 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 53 time to turn everything in is 1.290000 number of dielectric boundary points 80844 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 18327 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) : 2.087854 object centre at (A) : 11.84550 21.83300 18.44500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1581807 0.1217552 midg,1,midg; midg,igrid,midg 0.3261805 -6.6242464E-02 1,midg,midg; igrid,midg,midg 0.4431118 -0.3669644 gauss-seidel spectral radius is 0.9993016 estimated iterations to convergence 299 setup time was (sec) 1.520000 now iterating at: 12:13:31 rms-change max change #iterations 11.09440 480.8326 at 10iterations 6.561665 150.5919 at 20iterations 3.856576 70.23279 at 30iterations 2.281360 40.86653 at 40iterations 1.337754 26.49094 at 50iterations 0.7869539 13.95031 at 60iterations 0.4621469 7.083151 at 70iterations 0.2708460 4.427967 at 80iterations 0.1585394 2.519983 at 90iterations 9.2900038E-02 1.569343 at 100iterations 5.4371912E-02 0.9686985 at 110iterations 3.1829387E-02 0.5624360 at 120iterations 1.8659700E-02 0.3392487 at 130iterations 1.0930872E-02 0.2217064 at 140iterations 6.4092148E-03 0.1066589 at 150iterations 3.7947830E-03 6.4864874E-02 at 160iterations 2.2534842E-03 4.3437481E-02 at 170iterations 1.3677595E-03 2.8360367E-02 at 180iterations finished qdiffx linear iterations at : 12:13:42 total time elapsed so far: 12.77000 # loops : 180 mean,max change (kT/e) : 1.3677595E-03 2.8360367E-02 energy calculations done at 12.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.91000 DelPhi exited at 12:13:42 12.912u 0.194s 0:13.39 97.8% 0+0k 0+0io 0pf+0w