Sun Oct 9 10:35:30 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 10:35:30 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2926 !!! WARNING: CME 113 has a net charge of -0.3480 !!! WARNING: HIR 212 has a net charge of 0.5140 !!! WARNING: CME 218 has a net charge of -0.3480 !!! WARNING: CME 314 has a net charge of -0.3480 !!! WARNING: CME 463 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.1350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of -0.0350 !!! WARNING: CME 7 has a net charge of -0.0350 !!! WARNING: CME 9 has a net charge of -0.0350 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5826991 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): -17.90100 43.19400 ymin,ymax (A): -27.79600 25.50800 zmin,zma (A): -29.17000 27.26700 x,y,z range (A): 61.09500 53.30400 56.43700 scale (grids/A): 0.5826991 object centre (A): 12.64650 -1.143999 -0.9514999 number of atom coordinates read : 2926 total number of charged atoms : 2830 net assigned charge : 1.347026 assigned positive charge : 438.9619 centred at (gu) : 88.35577 90.82709 91.76682 assigned negative charge : -437.6168 centred at (gu) : 88.33353 90.77246 91.70799 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6934 nv = 96 ne = 84 npr = 55986 no. pairs analyzed = 55986 no. exposed pairs = 4142 no. arc points = 29024 no. surface atoms = 1376 nbur = 1550 mkacc time = 0.1300000 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 = 1.484000 m= 352 mr = 3437 m= 0 mr = 30 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3819 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2869 ## 305 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8622 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.2309886E-10 2.5344637E-09 midg,1,midg; midg,igrid,midg -8.2119300E-10 1.9060535E-09 1,midg,midg; igrid,midg,midg -3.5507672E-10 5.5682076E-10 gauss-seidel spectral radius is 0.9848075 estimated iterations to convergence 67 setup time was (sec) 0.5900000 now iterating at: 10:35:31 rms-change max change #iterations 0.1020334 14.87324 at 10iterations 8.1254449E-03 1.296200 at 20iterations 7.9224922E-04 0.1140747 at 30iterations 1.5018800E-04 2.3603439E-02 at 40iterations 4.1258794E-05 6.3815117E-03 at 50iterations finished qdiffx linear iterations at : 10:35:34 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 4.1258794E-05 6.3815117E-03 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.270000 DelPhi exited at 10:35:35 4.278u 0.292s 0:05.06 90.1% 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 Sun Oct 9 2011 at 10:35:35 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2926 !!! WARNING: CME 113 has a net charge of -0.3480 !!! WARNING: HIR 212 has a net charge of 0.5140 !!! WARNING: CME 218 has a net charge of -0.3480 !!! WARNING: CME 314 has a net charge of -0.3480 !!! WARNING: CME 463 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.1350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of -0.0350 !!! WARNING: CME 7 has a net charge of -0.0350 !!! WARNING: CME 9 has a net charge of -0.0350 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.748097 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): -17.90100 43.19400 ymin,ymax (A): -27.79600 25.50800 zmin,zma (A): -29.17000 27.26700 x,y,z range (A): 61.09500 53.30400 56.43700 scale (grids/A): 1.748097 object centre (A): 12.64650 -1.143999 -0.9514999 number of atom coordinates read : 2926 total number of charged atoms : 2830 net assigned charge : 1.347026 assigned positive charge : 438.9619 centred at (gu) : 85.06671 92.48048 95.29924 assigned negative charge : -437.6168 centred at (gu) : 85.00049 92.31728 95.12412 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 75809 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29024 grid for indexing accessible points = 1.400000 m= 25547 mr = 50747 m= 3480 mr = 17112 m= 129 mr = 1729 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 35356 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 236 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 21982 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) : 0.5826991 object centre at (A) : 12.64650 -1.143999 -0.9514999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3609084E-02 9.0878019E-03 midg,1,midg; midg,igrid,midg 1.0002603E-02 7.8056883E-03 1,midg,midg; igrid,midg,midg 3.0835607E-04 1.8265970E-03 gauss-seidel spectral radius is 0.9984396 estimated iterations to convergence 201 setup time was (sec) 1.020000 now iterating at: 10:35:36 rms-change max change #iterations 3.826970 182.0262 at 10iterations 1.686778 58.17068 at 20iterations 0.7466336 25.07932 at 30iterations 0.3307238 10.56383 at 40iterations 0.1468283 5.301259 at 50iterations 6.5209009E-02 2.335701 at 60iterations 2.9061470E-02 0.9760342 at 70iterations 1.2913208E-02 0.4153228 at 80iterations 5.7672681E-03 0.1826706 at 90iterations 2.5903648E-03 9.1590881E-02 at 100iterations 1.1814169E-03 3.8272858E-02 at 110iterations 5.4643163E-04 1.9678116E-02 at 120iterations finished qdiffx linear iterations at : 10:35:45 total time elapsed so far: 9.610000 # loops : 120 mean,max change (kT/e) : 5.4643163E-04 1.9678116E-02 energy calculations done at 9.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.800000 DelPhi exited at 10:35:45 9.802u 0.289s 0:10.35 97.3% 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 10:35:45 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2926 !!! WARNING: CME 113 has a net charge of -0.3480 !!! WARNING: HIR 212 has a net charge of 0.5140 !!! WARNING: CME 218 has a net charge of -0.3480 !!! WARNING: CME 314 has a net charge of -0.3480 !!! WARNING: CME 463 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.1350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of -0.0350 !!! WARNING: CME 7 has a net charge of -0.0350 !!! WARNING: CME 9 has a net charge of -0.0350 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.622146 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): -17.90100 43.19400 ymin,ymax (A): -27.79600 25.50800 zmin,zma (A): -29.17000 27.26700 x,y,z range (A): 61.09500 53.30400 56.43700 scale (grids/A): 2.622146 object centre (A): 12.64650 -1.143999 -0.9514999 number of atom coordinates read : 2926 total number of charged atoms : 2830 net assigned charge : 1.347026 assigned positive charge : 438.9619 centred at (gu) : 82.59978 93.72060 97.94864 assigned negative charge : -437.6168 centred at (gu) : 82.50080 93.47593 97.68604 start vw surface at 0.1600000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 175603 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29024 grid for indexing accessible points = 1.400000 m= 84534 mr = 124581 m= 27703 mr = 65501 m= 5790 mr = 20346 m= 549 mr = 3758 m= 17 mr = 239 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.490000 number of dielectric boundary points 79772 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 22628 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) : 1.748097 object centre at (A) : 12.64650 -1.143999 -0.9514999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1855575 8.8863142E-02 midg,1,midg; midg,igrid,midg 0.2274990 8.3279274E-02 1,midg,midg; igrid,midg,midg -4.4053141E-03 9.4257049E-02 gauss-seidel spectral radius is 0.9992189 estimated iterations to convergence 282 setup time was (sec) 1.830000 now iterating at: 10:35:47 rms-change max change #iterations 9.636502 277.2077 at 10iterations 5.650236 172.2344 at 20iterations 3.286602 75.43372 at 30iterations 1.899628 41.00266 at 40iterations 1.091186 21.13700 at 50iterations 0.6260291 12.36848 at 60iterations 0.3577636 8.770782 at 70iterations 0.2045534 4.232235 at 80iterations 0.1164222 2.134322 at 90iterations 6.6141665E-02 1.230621 at 100iterations 3.7688516E-02 0.7196598 at 110iterations 2.1412989E-02 0.4118137 at 120iterations 1.2202729E-02 0.2465382 at 130iterations 6.9534574E-03 0.1384144 at 140iterations 3.9724596E-03 7.6232910E-02 at 150iterations 2.2802034E-03 4.4889450E-02 at 160iterations 1.3272204E-03 2.9190063E-02 at 170iterations 7.8846992E-04 1.7149925E-02 at 180iterations finished qdiffx linear iterations at : 10:36:01 total time elapsed so far: 15.41000 # loops : 180 mean,max change (kT/e) : 7.8846992E-04 1.7149925E-02 energy calculations done at 15.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.59000 DelPhi exited at 10:36:02 15.592u 0.289s 0:16.26 97.6% 0+0k 0+0io 0pf+0w