Mon Oct 10 09:46:08 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+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 Mon Oct 10 2011 at 09:46:08 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3151 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: 0.5334533 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): 105.2420 171.9770 ymin,ymax (A): -42.60300 10.71300 zmin,zma (A): 42.05500 102.7550 x,y,z range (A): 66.73499 53.31600 60.70000 scale (grids/A): 0.5334533 object centre (A): 138.6095 -15.94500 72.40500 number of atom coordinates read : 3151 total number of charged atoms : 2992 net assigned charge : 10.00002 assigned positive charge : 461.5983 centred at (gu) : 90.43690 89.47136 89.46819 assigned negative charge : -451.5991 centred at (gu) : 90.40670 89.50213 89.34127 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5806 nv = 96 ne = 84 npr = 61874 no. pairs analyzed = 61874 no. exposed pairs = 4736 no. arc points = 33917 no. surface atoms = 1571 nbur = 1580 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 240 mr = 2474 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 0.3700000 number of dielectric boundary points 3571 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3328 ## 441 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 7663 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8625163E-10 7.8822293E-10 midg,1,midg; midg,igrid,midg 5.7869215E-10 2.2042125E-10 1,midg,midg; igrid,midg,midg 2.2744534E-10 5.6291910E-10 gauss-seidel spectral radius is 0.9819182 estimated iterations to convergence 61 setup time was (sec) 0.7000000 now iterating at: 09:46:10 rms-change max change #iterations 6.5298311E-02 13.23038 at 10iterations 4.0062405E-03 0.7059727 at 20iterations 2.7459188E-04 4.7192574E-02 at 30iterations 3.0992967E-05 3.8671494E-03 at 40iterations 6.0772713E-06 7.3528290E-04 at 50iterations finished qdiffx linear iterations at : 09:46:14 total time elapsed so far: 4.790000 # loops : 50 mean,max change (kT/e) : 6.0772713E-06 7.3528290E-04 energy calculations done at 4.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.960000 DelPhi exited at 09:46:14 4.960u 0.379s 0:05.60 95.1% 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 Mon Oct 10 2011 at 09:46:14 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3151 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: 1.600360 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): 105.2420 171.9770 ymin,ymax (A): -42.60300 10.71300 zmin,zma (A): 42.05500 102.7550 x,y,z range (A): 66.73499 53.31600 60.70000 scale (grids/A): 1.600360 object centre (A): 138.6095 -15.94500 72.40500 number of atom coordinates read : 3151 total number of charged atoms : 2992 net assigned charge : 10.00002 assigned positive charge : 461.5983 centred at (gu) : 91.31004 88.41335 88.40374 assigned negative charge : -451.5991 centred at (gu) : 91.21991 88.50602 88.02348 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 62748 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33917 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 18118 mr = 37729 m= 1819 mr = 11081 m= 59 mr = 677 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 33257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 393 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 22740 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) : 0.5334533 object centre at (A) : 138.6095 -15.94500 72.40500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2269447E-03 2.2245994E-02 midg,1,midg; midg,igrid,midg 9.6900249E-03 7.1221539E-03 1,midg,midg; igrid,midg,midg -3.5815372E-03 5.6758611E-03 gauss-seidel spectral radius is 0.9981459 estimated iterations to convergence 185 setup time was (sec) 0.8600000 now iterating at: 09:46:16 rms-change max change #iterations 3.211054 147.0820 at 10iterations 1.321014 54.90649 at 20iterations 0.5432593 25.44833 at 30iterations 0.2234534 8.156919 at 40iterations 9.2485495E-02 3.896412 at 50iterations 3.8135096E-02 1.519287 at 60iterations 1.5724534E-02 0.6408844 at 70iterations 6.5069101E-03 0.2619667 at 80iterations 2.6903460E-03 9.5541000E-02 at 90iterations 1.1147034E-03 4.0658951E-02 at 100iterations 4.5984983E-04 1.8441558E-02 at 110iterations 1.9177026E-04 7.3199272E-03 at 120iterations finished qdiffx linear iterations at : 09:46:27 total time elapsed so far: 11.12000 # loops : 120 mean,max change (kT/e) : 1.9177026E-04 7.3199272E-03 energy calculations done at 11.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.28000 DelPhi exited at 09:46:27 11.280u 0.467s 0:13.03 90.0% 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 Mon Oct 10 2011 at 09:46:27 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3151 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: 2.400540 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): 105.2420 171.9770 ymin,ymax (A): -42.60300 10.71300 zmin,zma (A): 42.05500 102.7550 x,y,z range (A): 66.73499 53.31600 60.70000 scale (grids/A): 2.400540 object centre (A): 138.6095 -15.94500 72.40500 number of atom coordinates read : 3151 total number of charged atoms : 2992 net assigned charge : 10.00002 assigned positive charge : 461.5983 centred at (gu) : 91.96490 87.61991 87.60530 assigned negative charge : -451.5991 centred at (gu) : 91.82981 87.75895 87.03511 start vw surface at 0.1400000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 145220 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33917 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 62099 mr = 93658 m= 17221 mr = 45499 m= 2571 mr = 11734 m= 140 mr = 1338 m= 4 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.330000 number of dielectric boundary points 75008 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 23899 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) : 1.600360 object centre at (A) : 138.6095 -15.94500 72.40500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.8183703E-02 0.4141518 midg,1,midg; midg,igrid,midg 0.1618620 0.1146397 1,midg,midg; igrid,midg,midg -3.9409030E-02 -8.9715131E-02 gauss-seidel spectral radius is 0.9991459 estimated iterations to convergence 270 setup time was (sec) 1.720000 now iterating at: 09:46:29 rms-change max change #iterations 8.625230 276.5375 at 10iterations 4.928082 149.1688 at 20iterations 2.793027 69.28156 at 30iterations 1.568614 42.58871 at 40iterations 0.8784959 23.24055 at 50iterations 0.4903103 11.76901 at 60iterations 0.2733541 7.343491 at 70iterations 0.1520528 3.505097 at 80iterations 8.4051356E-02 1.928942 at 90iterations 4.6546180E-02 1.112530 at 100iterations 2.5773315E-02 0.5606689 at 110iterations 1.4229278E-02 0.3491592 at 120iterations 7.8489659E-03 0.1892924 at 130iterations 4.3453160E-03 9.9384308E-02 at 140iterations 2.3926499E-03 4.9415588E-02 at 150iterations 1.3205626E-03 2.7368546E-02 at 160iterations 7.2800473E-04 1.5800476E-02 at 170iterations 4.0192946E-04 9.1443062E-03 at 180iterations finished qdiffx linear iterations at : 09:46:46 total time elapsed so far: 18.12000 # loops : 180 mean,max change (kT/e) : 4.0192946E-04 9.1443062E-03 energy calculations done at 18.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.30000 DelPhi exited at 09:46:46 18.302u 0.461s 0:19.05 98.4% 0+0k 0+0io 0pf+0w