Sun Oct 9 11:59:37 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 11:59:37 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 = 2380 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: 0.6978750 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): -6.376000 44.10900 ymin,ymax (A): -14.19400 36.81800 zmin,zma (A): 1.538000 44.64100 x,y,z range (A): 50.48500 51.01200 43.10300 scale (grids/A): 0.6978750 object centre (A): 18.86650 11.31200 23.08950 number of atom coordinates read : 2380 total number of charged atoms : 2239 net assigned charge : 4.500014 assigned positive charge : 362.5681 centred at (gu) : 89.58590 91.13566 90.91565 assigned negative charge : -358.0686 centred at (gu) : 89.59812 91.27695 91.00406 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7776 nv = 96 ne = 84 npr = 48127 no. pairs analyzed = 48127 no. exposed pairs = 2915 no. arc points = 20657 no. surface atoms = 987 nbur = 1393 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 506 mr = 4350 m= 5 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 55 time to turn everything in is 0.3000000 number of dielectric boundary points 3857 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1902 ## 175 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8804 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.9636925E-08 -1.1560902E-08 midg,1,midg; midg,igrid,midg 7.5898328E-08 -4.3302208E-08 1,midg,midg; igrid,midg,midg 4.0050228E-08 2.3896417E-08 gauss-seidel spectral radius is 0.9893299 estimated iterations to convergence 79 setup time was (sec) 0.5300000 now iterating at: 11:59:38 rms-change max change #iterations 0.2018993 33.61611 at 10iterations 2.4652123E-02 3.036058 at 20iterations 3.2211184E-03 0.4917068 at 30iterations 5.4351974E-04 9.7442627E-02 at 40iterations 1.3619942E-04 2.2092819E-02 at 50iterations finished qdiffx linear iterations at : 11:59:40 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 1.3619942E-04 2.2092819E-02 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 11:59:41 3.379u 0.229s 0:03.90 92.0% 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 11:59:41 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 = 2380 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: 2.093625 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): -6.376000 44.10900 ymin,ymax (A): -14.19400 36.81800 zmin,zma (A): 1.538000 44.64100 x,y,z range (A): 50.48500 51.01200 43.10300 scale (grids/A): 2.093625 object centre (A): 18.86650 11.31200 23.08950 number of atom coordinates read : 2380 total number of charged atoms : 2239 net assigned charge : 4.500014 assigned positive charge : 362.5681 centred at (gu) : 88.75711 93.40660 92.74667 assigned negative charge : -358.0686 centred at (gu) : 88.79439 93.83059 93.01191 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 82387 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20657 grid for indexing accessible points = 1.400000 m= 32474 mr = 57391 m= 6019 mr = 24357 m= 505 mr = 3905 m= 12 mr = 228 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1540 time to turn everything in is 0.6100000 number of dielectric boundary points 35516 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 17770 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) : 0.6978750 object centre at (A) : 18.86650 11.31200 23.08950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3119859E-02 1.6392855E-04 midg,1,midg; midg,igrid,midg 2.2669379E-02 -3.6960732E-02 1,midg,midg; igrid,midg,midg 3.9760388E-02 -1.3912539E-02 gauss-seidel spectral radius is 0.9988363 estimated iterations to convergence 232 setup time was (sec) 0.8900000 now iterating at: 11:59:42 rms-change max change #iterations 4.856795 217.9105 at 10iterations 2.395548 76.47446 at 20iterations 1.186500 33.09606 at 30iterations 0.5881681 17.42708 at 40iterations 0.2921894 11.82690 at 50iterations 0.1446491 4.294685 at 60iterations 7.1954489E-02 2.006651 at 70iterations 3.5779834E-02 1.115166 at 80iterations 1.7885575E-02 0.4885033 at 90iterations 8.9459009E-03 0.2672882 at 100iterations 4.5072543E-03 0.1287231 at 110iterations 2.3048804E-03 6.3934326E-02 at 120iterations finished qdiffx linear iterations at : 11:59:49 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 2.3048804E-03 6.3934326E-02 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 11:59:49 7.753u 0.248s 0:08.31 96.1% 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 11:59:49 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 = 2380 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: 3.140437 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): -6.376000 44.10900 ymin,ymax (A): -14.19400 36.81800 zmin,zma (A): 1.538000 44.64100 x,y,z range (A): 50.48500 51.01200 43.10300 scale (grids/A): 3.140437 object centre (A): 18.86650 11.31200 23.08950 number of atom coordinates read : 2380 total number of charged atoms : 2239 net assigned charge : 4.500014 assigned positive charge : 362.5681 centred at (gu) : 88.13562 95.10970 94.11987 assigned negative charge : -358.0686 centred at (gu) : 88.19147 95.74586 94.51782 start vw surface at 0.1500000 fill in re-entrant regions at 0.8500000 boundary points on vw surface= 189741 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20657 grid for indexing accessible points = 1.400000 m= 101610 mr = 138633 m= 40527 mr = 83731 m= 11404 mr = 32828 m= 2214 mr = 8700 m= 263 mr = 1592 m= 13 mr = 176 m= 0 mr = 7 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 5214 time to turn everything in is 1.880000 number of dielectric boundary points 80105 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.010000 number of grid points assigned charge 17912 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) : 2.093625 object centre at (A) : 18.86650 11.31200 23.08950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5437854 -0.1385584 midg,1,midg; midg,igrid,midg 0.4589850 -0.4091441 1,midg,midg; igrid,midg,midg 0.3597376 -0.3845954 gauss-seidel spectral radius is 0.9992993 estimated iterations to convergence 298 setup time was (sec) 2.180000 now iterating at: 11:59:52 rms-change max change #iterations 10.92983 323.1361 at 10iterations 6.482771 139.6318 at 20iterations 3.844520 89.33520 at 30iterations 2.267922 41.94227 at 40iterations 1.338197 23.65765 at 50iterations 0.7883189 12.94374 at 60iterations 0.4635779 8.126878 at 70iterations 0.2719273 4.441548 at 80iterations 0.1596735 2.781651 at 90iterations 9.3564741E-02 1.740898 at 100iterations 5.4905910E-02 0.9001198 at 110iterations 3.2339945E-02 0.5679703 at 120iterations 1.9158142E-02 0.3095169 at 130iterations 1.1428102E-02 0.1999283 at 140iterations 6.9698272E-03 0.1325340 at 150iterations 4.3770275E-03 8.4152222E-02 at 160iterations 2.8699427E-03 5.8601379E-02 at 170iterations 1.9958352E-03 4.2972565E-02 at 180iterations finished qdiffx linear iterations at : 12:00:04 total time elapsed so far: 14.60000 # loops : 180 mean,max change (kT/e) : 1.9958352E-03 4.2972565E-02 energy calculations done at 14.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.77000 DelPhi exited at 12:00:05 14.771u 0.269s 0:15.39 97.6% 0+0k 0+0io 0pf+0w