Sun Oct 9 08:48:40 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 Sun Oct 9 2011 at 08:48:40 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 = 5418 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: 0.5174268 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): -33.70200 35.10000 ymin,ymax (A): -33.26700 31.44400 zmin,zma (A): -11.41200 52.59900 x,y,z range (A): 68.80200 64.71100 64.01100 scale (grids/A): 0.5174268 object centre (A): 0.6989994 -0.9114990 20.59350 number of atom coordinates read : 5418 total number of charged atoms : 5253 net assigned charge : -1.999972 assigned positive charge : 811.6801 centred at (gu) : 90.00927 88.73672 90.15624 assigned negative charge : -813.6867 centred at (gu) : 90.11597 88.71046 90.24696 start vw surface at 0.2400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 9076 nv = 96 ne = 84 npr = 110200 no. pairs analyzed = 110200 no. exposed pairs = 6970 no. arc points = 47869 no. surface atoms = 2328 nbur = 3090 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 = 1.652000 m= 331 mr = 4599 m= 0 mr = 11 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.5200000 number of dielectric boundary points 4797 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4633 ## 650 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 12263 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0413752E-10 -4.1395271E-10 midg,1,midg; midg,igrid,midg -1.9464531E-10 4.7822395E-11 1,midg,midg; igrid,midg,midg 3.7741701E-10 -4.6299059E-10 gauss-seidel spectral radius is 0.9809412 estimated iterations to convergence 60 setup time was (sec) 0.7300000 now iterating at: 08:48:41 rms-change max change #iterations 7.7166878E-02 14.12210 at 10iterations 4.5094835E-03 0.6610489 at 20iterations 3.7702746E-04 6.0020447E-02 at 30iterations 7.4285890E-05 1.4658928E-02 at 40iterations 2.0880421E-05 3.8542747E-03 at 50iterations finished qdiffx linear iterations at : 08:48:43 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 2.0880421E-05 3.8542747E-03 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 08:48:44 3.303u 0.147s 0:03.75 91.7% 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 08:48:44 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 = 5418 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: 1.552280 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): -33.70200 35.10000 ymin,ymax (A): -33.26700 31.44400 zmin,zma (A): -11.41200 52.59900 x,y,z range (A): 68.80200 64.71100 64.01100 scale (grids/A): 1.552280 object centre (A): 0.6989994 -0.9114990 20.59350 number of atom coordinates read : 5418 total number of charged atoms : 5253 net assigned charge : -1.999972 assigned positive charge : 811.6801 centred at (gu) : 90.02580 86.20836 90.46690 assigned negative charge : -813.6867 centred at (gu) : 90.34772 86.13091 90.74109 start vw surface at 0.2100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 102589 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47869 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 29376 mr = 69959 m= 2605 mr = 18905 m= 52 mr = 1082 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1539 time to turn everything in is 0.7000000 number of dielectric boundary points 44676 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 620 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 39615 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) : 0.5174268 object centre at (A) : 0.6989994 -0.9114990 20.59350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0712583E-03 -6.2259356E-03 midg,1,midg; midg,igrid,midg -1.7182295E-03 -2.9102126E-03 1,midg,midg; igrid,midg,midg 5.4915701E-03 -2.0899180E-02 gauss-seidel spectral radius is 0.9982294 estimated iterations to convergence 189 setup time was (sec) 0.9800000 now iterating at: 08:48:45 rms-change max change #iterations 4.201380 151.9638 at 10iterations 1.775137 60.10794 at 20iterations 0.7493534 22.89538 at 30iterations 0.3162265 10.09194 at 40iterations 0.1335208 4.146572 at 50iterations 5.6498162E-02 1.646390 at 60iterations 2.3764627E-02 0.6736636 at 70iterations 1.0113314E-02 0.3719482 at 80iterations 4.2589749E-03 0.1292467 at 90iterations 1.8124883E-03 5.2093506E-02 at 100iterations 7.7298994E-04 2.2508621E-02 at 110iterations 3.3033561E-04 9.7402334E-03 at 120iterations finished qdiffx linear iterations at : 08:48:52 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 3.3033561E-04 9.7402334E-03 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 08:48:52 7.740u 0.269s 0:08.30 96.3% 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 08:48:52 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 = 5418 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: 2.328421 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): -33.70200 35.10000 ymin,ymax (A): -33.26700 31.44400 zmin,zma (A): -11.41200 52.59900 x,y,z range (A): 68.80200 64.71100 64.01100 scale (grids/A): 2.328421 object centre (A): 0.6989994 -0.9114990 20.59350 number of atom coordinates read : 5418 total number of charged atoms : 5253 net assigned charge : -1.999972 assigned positive charge : 811.6801 centred at (gu) : 90.03833 84.31202 90.70004 assigned negative charge : -813.6867 centred at (gu) : 90.52148 84.19630 91.11155 start vw surface at 0.2100000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 239162 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47869 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 105452 mr = 172427 m= 26426 mr = 80716 m= 3679 mr = 18518 m= 197 mr = 2269 m= 2 mr = 53 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 4771 time to turn everything in is 1.650000 number of dielectric boundary points 100936 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 65 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 41922 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) : 1.552280 object centre at (A) : 0.6989994 -0.9114990 20.59350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2688682 -0.1635466 midg,1,midg; midg,igrid,midg -1.1345825E-02 -3.9229222E-02 1,midg,midg; igrid,midg,midg 5.8250029E-02 -0.5681009 gauss-seidel spectral radius is 0.9992208 estimated iterations to convergence 283 setup time was (sec) 1.940000 now iterating at: 08:48:54 rms-change max change #iterations 11.35906 409.5329 at 10iterations 6.691837 194.6419 at 20iterations 3.914452 91.51048 at 30iterations 2.278230 50.55561 at 40iterations 1.320272 26.99084 at 50iterations 0.7635288 15.69497 at 60iterations 0.4396512 9.266294 at 70iterations 0.2529576 5.175530 at 80iterations 0.1448481 2.979296 at 90iterations 8.2996450E-02 1.647110 at 100iterations 4.7503278E-02 0.8417055 at 110iterations 2.7183365E-02 0.5163145 at 120iterations 1.5494452E-02 0.2690964 at 130iterations 8.8412119E-03 0.1792088 at 140iterations 5.0531584E-03 9.4967782E-02 at 150iterations 2.8901387E-03 5.0167084E-02 at 160iterations 1.6511041E-03 3.1615257E-02 at 170iterations 9.4546576E-04 1.4992267E-02 at 180iterations finished qdiffx linear iterations at : 08:49:04 total time elapsed so far: 11.79000 # loops : 180 mean,max change (kT/e) : 9.4546576E-04 1.4992267E-02 energy calculations done at 11.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.97000 DelPhi exited at 08:49:05 11.974u 0.202s 0:12.46 97.6% 0+0k 0+0io 0pf+0w