Sat Oct 15 12:44:23 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 Sat Oct 15 2011 at 12:44:23 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5751 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1800000 grid size : 179 scale,in grids/A, set to be: 0.4819016 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): 3.728000 77.60200 ymin,ymax (A): 22.55300 85.83700 zmin,zma (A): 6.411000 70.62200 x,y,z range (A): 73.87400 63.28400 64.21100 scale (grids/A): 0.4819016 object centre (A): 40.66500 54.19500 38.51650 number of atom coordinates read : 5751 total number of charged atoms : 5585 net assigned charge : 1.000034 assigned positive charge : 866.0237 centred at (gu) : 89.89091 88.45094 89.23208 assigned negative charge : -865.0308 centred at (gu) : 89.73571 88.44128 89.14611 start vw surface at 0.2600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 8281 nv = 96 ne = 84 npr = 115000 no. pairs analyzed = 115000 no. exposed pairs = 7306 no. arc points = 51021 no. surface atoms = 2437 nbur = 3314 mkacc time = 0.3900000 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 = 1.792000 m= 255 mr = 4131 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.7300000 number of dielectric boundary points 4399 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4735 ## 798 charges are in solution ## iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 11260 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.6501917E-11 6.2236362E-11 midg,1,midg; midg,igrid,midg -5.5988378E-12 8.4307951E-12 1,midg,midg; igrid,midg,midg -1.3474410E-10 1.3021129E-10 gauss-seidel spectral radius is 0.9780601 estimated iterations to convergence 56 setup time was (sec) 1.100000 now iterating at: 12:44:26 rms-change max change #iterations 5.5017959E-02 7.763604 at 10iterations 2.7794500E-03 0.4262421 at 20iterations 2.4739045E-04 5.3407669E-02 at 30iterations 5.5083670E-05 1.2172699E-02 at 40iterations 1.5546928E-05 3.1051636E-03 at 50iterations finished qdiffx linear iterations at : 12:44:31 total time elapsed so far: 5.410000 # loops : 50 mean,max change (kT/e) : 1.5546928E-05 3.1051636E-03 energy calculations done at 5.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.630000 DelPhi exited at 12:44:31 5.631u 0.437s 0:08.17 74.1% 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 15 2011 at 12:44:31 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5751 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1800000 grid size : 179 scale,in grids/A, set to be: 1.445705 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): 3.728000 77.60200 ymin,ymax (A): 22.55300 85.83700 zmin,zma (A): 6.411000 70.62200 x,y,z range (A): 73.87400 63.28400 64.21100 scale (grids/A): 1.445705 object centre (A): 40.66500 54.19500 38.51650 number of atom coordinates read : 5751 total number of charged atoms : 5585 net assigned charge : 1.000034 assigned positive charge : 866.0237 centred at (gu) : 89.67121 85.35117 87.69437 assigned negative charge : -865.0308 centred at (gu) : 89.20696 85.32359 87.43789 start vw surface at 0.2600000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 94975 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51021 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 24930 mr = 64276 m= 1691 mr = 15706 m= 35 mr = 590 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 1741 time to turn everything in is 1.000000 number of dielectric boundary points 41059 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 809 ## 14 charges are in solution ## iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 41010 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) : 0.4819016 object centre at (A) : 40.66500 54.19500 38.51650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6985331E-03 5.9061581E-03 midg,1,midg; midg,igrid,midg -1.2593893E-03 -2.3927554E-03 1,midg,midg; igrid,midg,midg -8.2076294E-03 2.0033913E-02 gauss-seidel spectral radius is 0.9979421 estimated iterations to convergence 175 setup time was (sec) 1.350000 now iterating at: 12:44:33 rms-change max change #iterations 3.664515 131.7414 at 10iterations 1.443995 48.73898 at 20iterations 0.5698186 18.66210 at 30iterations 0.2253714 7.621362 at 40iterations 8.8556185E-02 2.807266 at 50iterations 3.4988683E-02 1.137489 at 60iterations 1.3911454E-02 0.4660978 at 70iterations 5.5220849E-03 0.1865959 at 80iterations 2.2179894E-03 6.9880486E-02 at 90iterations 9.0608076E-04 3.3916473E-02 at 100iterations 3.8620681E-04 1.4015198E-02 at 110iterations 1.7874262E-04 6.7481995E-03 at 120iterations finished qdiffx linear iterations at : 12:44:53 total time elapsed so far: 12.13000 # loops : 120 mean,max change (kT/e) : 1.7874262E-04 6.7481995E-03 energy calculations done at 12.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.33000 DelPhi exited at 12:44:55 12.335u 0.533s 0:23.41 54.9% 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 15 2011 at 12:44:55 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5751 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1800000 grid size : 179 scale,in grids/A, set to be: 2.168557 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): 3.728000 77.60200 ymin,ymax (A): 22.55300 85.83700 zmin,zma (A): 6.411000 70.62200 x,y,z range (A): 73.87400 63.28400 64.21100 scale (grids/A): 2.168557 object centre (A): 40.66500 54.19500 38.51650 number of atom coordinates read : 5751 total number of charged atoms : 5585 net assigned charge : 1.000034 assigned positive charge : 866.0237 centred at (gu) : 89.50624 83.02636 86.54104 assigned negative charge : -865.0308 centred at (gu) : 88.81051 82.98522 86.15692 start vw surface at 0.2600000 fill in re-entrant regions at 0.7800000 boundary points on vw surface= 221970 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51021 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 93576 mr = 159141 m= 20122 mr = 71117 m= 2097 mr = 13763 m= 68 mr = 1173 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 1.490000 no. cavity mid-points inaccessible to solvent = 5686 time to turn everything in is 2.430000 number of dielectric boundary points 92626 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 122 iepsmp to db, and charging done at 2.640000 number of grid points assigned charge 44446 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) : 1.445705 object centre at (A) : 40.66500 54.19500 38.51650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1295030 7.9519168E-02 midg,1,midg; midg,igrid,midg -2.2473462E-02 -3.4659721E-02 1,midg,midg; igrid,midg,midg -2.0686602E-02 0.3265959 gauss-seidel spectral radius is 0.9991381 estimated iterations to convergence 269 setup time was (sec) 2.870000 now iterating at: 12:45:00 rms-change max change #iterations 10.42876 268.5163 at 10iterations 5.965110 134.5227 at 20iterations 3.388603 71.66827 at 30iterations 1.907044 41.76829 at 40iterations 1.077138 24.34072 at 50iterations 0.6016387 14.14267 at 60iterations 0.3365026 8.786565 at 70iterations 0.1876400 3.583570 at 80iterations 0.1045694 2.046303 at 90iterations 5.8172245E-02 1.255656 at 100iterations 3.2305669E-02 0.6074104 at 110iterations 1.7879536E-02 0.4046631 at 120iterations 9.9199573E-03 0.1855888 at 130iterations 5.4977750E-03 0.1077155 at 140iterations 3.0402294E-03 5.7024002E-02 at 150iterations 1.6870335E-03 3.2045722E-02 at 160iterations 9.3665195E-04 1.6990662E-02 at 170iterations 5.2201882E-04 9.4356537E-03 at 180iterations finished qdiffx linear iterations at : 12:45:19 total time elapsed so far: 21.60000 # loops : 180 mean,max change (kT/e) : 5.2201882E-04 9.4356537E-03 energy calculations done at 21.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.81000 DelPhi exited at 12:45:20 21.813u 0.553s 0:25.40 88.0% 0+0k 0+0io 0pf+0w