Sun Oct 9 08:21:01 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 Sun Oct 9 2011 at 08:21:01 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5629 !!! WARNING: HIR 88 has a net charge of 0.5140 !!! WARNING: HIR 702 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5001053 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): -18.30700 46.78700 ymin,ymax (A): -33.86900 32.16300 zmin,zma (A): 3.131000 74.31600 x,y,z range (A): 65.09400 66.03200 71.18501 scale (grids/A): 0.5001053 object centre (A): 14.24000 -0.8529987 38.72350 number of atom coordinates read : 5629 total number of charged atoms : 5461 net assigned charge : -6.471982 assigned positive charge : 845.6478 centred at (gu) : 89.47822 88.92479 89.31120 assigned negative charge : -852.1267 centred at (gu) : 89.52179 88.92812 89.22314 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8919 nv = 96 ne = 84 npr = 113410 no. pairs analyzed = 113410 no. exposed pairs = 7075 no. arc points = 49165 no. surface atoms = 2368 nbur = 3261 mkacc time = 0.2400000 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 = 1.708000 m= 279 mr = 4527 m= 0 mr = 10 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.5000000 number of dielectric boundary points 4661 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4783 ## 740 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 11991 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7750560E-10 9.4165474E-11 midg,1,midg; midg,igrid,midg -6.5611329E-11 -4.7275010E-11 1,midg,midg; igrid,midg,midg 3.3379712E-11 -1.2326297E-10 gauss-seidel spectral radius is 0.9796184 estimated iterations to convergence 58 setup time was (sec) 0.7300000 now iterating at: 08:21:02 rms-change max change #iterations 6.6522196E-02 10.52057 at 10iterations 4.3098060E-03 0.7666130 at 20iterations 6.8916875E-04 0.1611366 at 30iterations 1.9390452E-04 4.4254303E-02 at 40iterations 6.0023987E-05 1.2722015E-02 at 50iterations finished qdiffx linear iterations at : 08:21:05 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 6.0023987E-05 1.2722015E-02 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 08:21:05 3.498u 0.200s 0:04.11 89.7% 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 08:21:05 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5629 !!! WARNING: HIR 88 has a net charge of 0.5140 !!! WARNING: HIR 702 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.500316 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): -18.30700 46.78700 ymin,ymax (A): -33.86900 32.16300 zmin,zma (A): 3.131000 74.31600 x,y,z range (A): 65.09400 66.03200 71.18501 scale (grids/A): 1.500316 object centre (A): 14.24000 -0.8529987 38.72350 number of atom coordinates read : 5629 total number of charged atoms : 5461 net assigned charge : -6.471982 assigned positive charge : 845.6478 centred at (gu) : 88.43250 86.77248 87.93177 assigned negative charge : -852.1267 centred at (gu) : 88.56533 86.78406 87.66943 start vw surface at 0.2100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 100936 reading accessible surface arcs data from file ARCDAT no. of arc points read = 49165 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 28382 mr = 68943 m= 2304 mr = 18361 m= 44 mr = 927 m= 0 mr = 2 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 278 time to turn everything in is 0.7000000 number of dielectric boundary points 43433 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 733 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 40754 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) : 0.5001053 object centre at (A) : 14.24000 -0.8529987 38.72350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3169689E-02 3.8929773E-03 midg,1,midg; midg,igrid,midg -5.0753416E-03 -7.5386758E-03 1,midg,midg; igrid,midg,midg 2.1182483E-03 2.1446105E-03 gauss-seidel spectral radius is 0.9981074 estimated iterations to convergence 183 setup time was (sec) 1.000000 now iterating at: 08:21:06 rms-change max change #iterations 3.984847 180.8038 at 10iterations 1.633872 49.25291 at 20iterations 0.6707641 22.46684 at 30iterations 0.2748824 9.050766 at 40iterations 0.1123648 3.397045 at 50iterations 4.6349172E-02 1.499512 at 60iterations 1.9089736E-02 0.5450783 at 70iterations 7.8836912E-03 0.2419472 at 80iterations 3.2816334E-03 0.1129303 at 90iterations 1.3959601E-03 4.7317505E-02 at 100iterations 6.1246590E-04 2.0824432E-02 at 110iterations 2.8837431E-04 1.1337280E-02 at 120iterations finished qdiffx linear iterations at : 08:21:13 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 2.8837431E-04 1.1337280E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 08:21:14 7.825u 0.216s 0:08.34 96.2% 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 08:21:14 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5629 !!! WARNING: HIR 88 has a net charge of 0.5140 !!! WARNING: HIR 702 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.250474 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): -18.30700 46.78700 ymin,ymax (A): -33.86900 32.16300 zmin,zma (A): 3.131000 74.31600 x,y,z range (A): 65.09400 66.03200 71.18501 scale (grids/A): 2.250474 object centre (A): 14.24000 -0.8529987 38.72350 number of atom coordinates read : 5629 total number of charged atoms : 5461 net assigned charge : -6.471982 assigned positive charge : 845.6478 centred at (gu) : 87.64835 85.15844 86.89716 assigned negative charge : -852.1267 centred at (gu) : 87.84789 85.17579 86.50422 start vw surface at 0.2200000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 234977 reading accessible surface arcs data from file ARCDAT no. of arc points read = 49165 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 103684 mr = 169598 m= 24827 mr = 79849 m= 3294 mr = 17472 m= 149 mr = 1951 m= 0 mr = 46 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 961 time to turn everything in is 1.700000 number of dielectric boundary points 98015 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 43549 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) : 1.500316 object centre at (A) : 14.24000 -0.8529987 38.72350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4058401 7.0193157E-02 midg,1,midg; midg,igrid,midg -0.1309393 -0.1477507 1,midg,midg; igrid,midg,midg 0.1003031 0.1410393 gauss-seidel spectral radius is 0.9991882 estimated iterations to convergence 277 setup time was (sec) 2.020000 now iterating at: 08:21:16 rms-change max change #iterations 11.01444 307.8636 at 10iterations 6.407715 148.0610 at 20iterations 3.702668 79.01018 at 30iterations 2.131367 45.12821 at 40iterations 1.222420 24.08813 at 50iterations 0.6975854 13.39237 at 60iterations 0.3967278 7.271212 at 70iterations 0.2254754 4.180361 at 80iterations 0.1280842 2.381626 at 90iterations 7.2544225E-02 1.286644 at 100iterations 4.1051514E-02 0.7719107 at 110iterations 2.3198999E-02 0.4417973 at 120iterations 1.3114629E-02 0.2468719 at 130iterations 7.4033495E-03 0.1450300 at 140iterations 4.1886242E-03 7.3767662E-02 at 150iterations 2.3711028E-03 4.2411804E-02 at 160iterations 1.3465168E-03 2.4247169E-02 at 170iterations 7.6932315E-04 1.3470650E-02 at 180iterations finished qdiffx linear iterations at : 08:21:27 total time elapsed so far: 12.87000 # loops : 180 mean,max change (kT/e) : 7.6932315E-04 1.3470650E-02 energy calculations done at 12.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.05000 DelPhi exited at 08:21:27 13.048u 0.253s 0:13.56 98.0% 0+0k 0+0io 0pf+0w