Sat Oct 8 11:34:57 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 Sat Oct 8 2011 at 11:34:57 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 = 4209 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: 0.5508789 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): -3.452000 61.17200 ymin,ymax (A): -12.89400 38.37500 zmin,zma (A): -18.55500 45.07300 x,y,z range (A): 64.62400 51.26900 63.62800 scale (grids/A): 0.5508789 object centre (A): 28.86000 12.74050 13.25900 number of atom coordinates read : 4209 total number of charged atoms : 4056 net assigned charge : -2.499936 assigned positive charge : 631.3329 centred at (gu) : 89.12633 89.94255 90.57424 assigned negative charge : -633.8354 centred at (gu) : 89.18959 90.03448 90.64464 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8168 nv = 96 ne = 84 npr = 88802 no. pairs analyzed = 88802 no. exposed pairs = 4850 no. arc points = 32305 no. surface atoms = 1659 nbur = 2550 mkacc time = 0.1600000 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 = 1.540000 m= 314 mr = 4621 m= 2 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3844 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3358 ## 396 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 10825 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2132526E-10 -1.1491934E-09 midg,1,midg; midg,igrid,midg 8.5467461E-10 -1.2283070E-09 1,midg,midg; igrid,midg,midg 6.5370875E-10 -7.3706963E-10 gauss-seidel spectral radius is 0.9830918 estimated iterations to convergence 63 setup time was (sec) 0.5100000 now iterating at: 11:34:59 rms-change max change #iterations 9.1132440E-02 12.76040 at 10iterations 6.6255149E-03 0.9412689 at 20iterations 8.3623495E-04 0.1117783 at 30iterations 2.3969292E-04 3.2291412E-02 at 40iterations 8.1135964E-05 1.1705399E-02 at 50iterations finished qdiffx linear iterations at : 11:35:02 total time elapsed so far: 3.740000 # loops : 50 mean,max change (kT/e) : 8.1135964E-05 1.1705399E-02 energy calculations done at 3.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.880000 DelPhi exited at 11:35:02 3.880u 0.206s 0:04.86 83.9% 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 Sat Oct 8 2011 at 11:35:02 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 = 4209 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: 1.652637 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): -3.452000 61.17200 ymin,ymax (A): -12.89400 38.37500 zmin,zma (A): -18.55500 45.07300 x,y,z range (A): 64.62400 51.26900 63.62800 scale (grids/A): 1.652637 object centre (A): 28.86000 12.74050 13.25900 number of atom coordinates read : 4209 total number of charged atoms : 4056 net assigned charge : -2.499936 assigned positive charge : 631.3329 centred at (gu) : 87.37758 89.82649 91.72156 assigned negative charge : -633.8354 centred at (gu) : 87.56811 90.10287 91.93340 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 91626 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32305 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 29590 mr = 66176 m= 3197 mr = 21194 m= 104 mr = 1668 m= 2 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1548 time to turn everything in is 0.4700000 number of dielectric boundary points 35470 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 317 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 31118 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) : 0.5508789 object centre at (A) : 28.86000 12.74050 13.25900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.1237457E-04 -1.3950934E-02 midg,1,midg; midg,igrid,midg 4.0714685E-03 -1.9350883E-02 1,midg,midg; igrid,midg,midg 1.8651992E-02 2.1387706E-02 gauss-seidel spectral radius is 0.9983432 estimated iterations to convergence 195 setup time was (sec) 0.7200000 now iterating at: 11:35:03 rms-change max change #iterations 4.134559 194.1206 at 10iterations 1.788410 59.75197 at 20iterations 0.7781734 26.02887 at 30iterations 0.3376904 10.62206 at 40iterations 0.1468697 4.220954 at 50iterations 6.3860029E-02 1.989923 at 60iterations 2.7882202E-02 1.016812 at 70iterations 1.2243958E-02 0.3710670 at 80iterations 5.3982390E-03 0.1609020 at 90iterations 2.4412766E-03 7.8880787E-02 at 100iterations 1.1424371E-03 3.5201073E-02 at 110iterations 5.7370967E-04 1.8357277E-02 at 120iterations finished qdiffx linear iterations at : 11:35:12 total time elapsed so far: 8.940000 # loops : 120 mean,max change (kT/e) : 5.7370967E-04 1.8357277E-02 energy calculations done at 8.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.070000 DelPhi exited at 11:35:12 9.076u 0.255s 0:09.59 97.1% 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 Sat Oct 8 2011 at 11:35:12 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 = 4209 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: 2.478955 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): -3.452000 61.17200 ymin,ymax (A): -12.89400 38.37500 zmin,zma (A): -18.55500 45.07300 x,y,z range (A): 64.62400 51.26900 63.62800 scale (grids/A): 2.478955 object centre (A): 28.86000 12.74050 13.25900 number of atom coordinates read : 4209 total number of charged atoms : 4056 net assigned charge : -2.499936 assigned positive charge : 631.3329 centred at (gu) : 86.06592 89.73953 92.58210 assigned negative charge : -633.8354 centred at (gu) : 86.35214 90.15421 92.89993 start vw surface at 0.1100000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 213367 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32305 grid for indexing accessible points = 1.400000 m= 103015 mr = 161445 m= 29836 mr = 83716 m= 5141 mr = 22950 m= 395 mr = 3548 m= 12 mr = 159 m= 0 mr = 3 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 5307 time to turn everything in is 1.170000 number of dielectric boundary points 79945 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 32414 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) : 1.652637 object centre at (A) : 28.86000 12.74050 13.25900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2845517 -0.2781021 midg,1,midg; midg,igrid,midg 4.6211261E-02 -0.2606614 1,midg,midg; igrid,midg,midg 0.4295000 0.2967781 gauss-seidel spectral radius is 0.9992102 estimated iterations to convergence 281 setup time was (sec) 1.470000 now iterating at: 11:35:14 rms-change max change #iterations 10.64063 250.9069 at 10iterations 6.146040 122.4546 at 20iterations 3.526960 69.91726 at 30iterations 2.019172 41.39875 at 40iterations 1.152621 22.80735 at 50iterations 0.6565062 12.42839 at 60iterations 0.3726438 6.768536 at 70iterations 0.2113665 3.609497 at 80iterations 0.1197171 2.624226 at 90iterations 6.7865640E-02 1.222060 at 100iterations 3.8422871E-02 0.7164841 at 110iterations 2.1773797E-02 0.4015598 at 120iterations 1.2338970E-02 0.2302217 at 130iterations 7.0138900E-03 0.1177406 at 140iterations 4.0091723E-03 7.5077534E-02 at 150iterations 2.3093801E-03 4.1481018E-02 at 160iterations 1.3480256E-03 2.6676178E-02 at 170iterations 8.1000273E-04 1.4005661E-02 at 180iterations finished qdiffx linear iterations at : 11:35:27 total time elapsed so far: 15.04000 # loops : 180 mean,max change (kT/e) : 8.1000273E-04 1.4005661E-02 energy calculations done at 15.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.18000 DelPhi exited at 11:35:28 15.177u 0.299s 0:15.85 97.5% 0+0k 0+0io 0pf+0w