Mon Oct 10 19:33:28 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 Mon Oct 10 2011 at 19:33:28 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 = 2983 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5475913 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): -26.48100 29.36800 ymin,ymax (A): -19.94100 26.49000 zmin,zma (A): 9.105000 74.11700 x,y,z range (A): 55.84900 46.43100 65.01199 scale (grids/A): 0.5475913 object centre (A): 1.443500 3.274500 41.61100 number of atom coordinates read : 2983 total number of charged atoms : 2841 net assigned charge : -0.4999706 assigned positive charge : 443.7832 centred at (gu) : 89.58396 90.35180 89.82621 assigned negative charge : -444.2844 centred at (gu) : 89.59983 90.24372 89.85775 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5845 nv = 96 ne = 84 npr = 58567 no. pairs analyzed = 58567 no. exposed pairs = 4045 no. arc points = 28783 no. surface atoms = 1325 nbur = 1658 mkacc time = 0.1000000 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= 276 mr = 2895 m= 3 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3215 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2938 ## 388 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7738 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9334839E-10 -2.4914537E-10 midg,1,midg; midg,igrid,midg -7.4166046E-10 7.8223594E-10 1,midg,midg; igrid,midg,midg 8.3559888E-11 -1.3432794E-10 gauss-seidel spectral radius is 0.9828118 estimated iterations to convergence 63 setup time was (sec) 0.4500000 now iterating at: 19:33:28 rms-change max change #iterations 7.2747506E-02 12.97687 at 10iterations 5.1260311E-03 0.8071356 at 20iterations 5.3521554E-04 9.8022461E-02 at 30iterations 1.2208273E-04 2.2701263E-02 at 40iterations 3.3106462E-05 6.2294006E-03 at 50iterations finished qdiffx linear iterations at : 19:33:32 total time elapsed so far: 3.580000 # loops : 50 mean,max change (kT/e) : 3.3106462E-05 6.2294006E-03 energy calculations done at 3.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.700000 DelPhi exited at 19:33:32 3.708u 0.231s 0:04.35 90.3% 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 Mon Oct 10 2011 at 19:33:32 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 = 2983 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.642774 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): -26.48100 29.36800 ymin,ymax (A): -19.94100 26.49000 zmin,zma (A): 9.105000 74.11700 x,y,z range (A): 55.84900 46.43100 65.01199 scale (grids/A): 1.642774 object centre (A): 1.443500 3.274500 41.61100 number of atom coordinates read : 2983 total number of charged atoms : 2841 net assigned charge : -0.4999706 assigned positive charge : 443.7832 centred at (gu) : 88.75118 91.05479 89.47797 assigned negative charge : -444.2844 centred at (gu) : 88.79900 90.73093 89.57311 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 64024 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28783 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 20407 mr = 41878 m= 2399 mr = 13894 m= 76 mr = 1239 m= 0 mr = 7 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 29888 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 303 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 21820 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) : 0.5475913 object centre at (A) : 1.443500 3.274500 41.61100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7948823E-03 -5.0394437E-03 midg,1,midg; midg,igrid,midg -4.6962015E-03 9.6549299E-03 1,midg,midg; igrid,midg,midg -4.0965234E-03 2.1205485E-04 gauss-seidel spectral radius is 0.9982193 estimated iterations to convergence 188 setup time was (sec) 0.6000000 now iterating at: 19:33:33 rms-change max change #iterations 3.337517 139.9595 at 10iterations 1.396742 55.75740 at 20iterations 0.5881124 22.32412 at 30iterations 0.2464818 9.168030 at 40iterations 0.1038839 3.463802 at 50iterations 4.3565981E-02 1.614525 at 60iterations 1.8352231E-02 0.6475873 at 70iterations 7.7376696E-03 0.3426495 at 80iterations 3.2960107E-03 0.1404854 at 90iterations 1.4166507E-03 5.4592133E-02 at 100iterations 6.2464183E-04 2.3256302E-02 at 110iterations 2.8991219E-04 1.2861252E-02 at 120iterations finished qdiffx linear iterations at : 19:33:41 total time elapsed so far: 8.330000 # loops : 120 mean,max change (kT/e) : 2.8991219E-04 1.2861252E-02 energy calculations done at 8.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.460000 DelPhi exited at 19:33:42 8.462u 0.243s 0:09.42 92.3% 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 Mon Oct 10 2011 at 19:33:42 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 = 2983 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.464161 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): -26.48100 29.36800 ymin,ymax (A): -19.94100 26.49000 zmin,zma (A): 9.105000 74.11700 x,y,z range (A): 55.84900 46.43100 65.01199 scale (grids/A): 2.464161 object centre (A): 1.443500 3.274500 41.61100 number of atom coordinates read : 2983 total number of charged atoms : 2841 net assigned charge : -0.4999706 assigned positive charge : 443.7832 centred at (gu) : 88.12666 91.58202 89.21694 assigned negative charge : -444.2844 centred at (gu) : 88.19838 91.09638 89.35959 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 148533 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28783 grid for indexing accessible points = 1.400000 m= 68630 mr = 103147 m= 21120 mr = 53332 m= 3857 mr = 15815 m= 283 mr = 2626 m= 2 mr = 123 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8300000 number of dielectric boundary points 67382 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 22705 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) : 1.642774 object centre at (A) : 1.443500 3.274500 41.61100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.0546290E-02 3.3012111E-02 midg,1,midg; midg,igrid,midg -5.1382668E-02 0.1208644 1,midg,midg; igrid,midg,midg -8.7581147E-03 2.7444497E-02 gauss-seidel spectral radius is 0.9991530 estimated iterations to convergence 271 setup time was (sec) 1.110000 now iterating at: 19:33:43 rms-change max change #iterations 8.544340 392.3848 at 10iterations 4.765347 124.3321 at 20iterations 2.653159 71.71232 at 30iterations 1.479757 40.38806 at 40iterations 0.8215420 18.83408 at 50iterations 0.4556697 11.16859 at 60iterations 0.2528540 5.783438 at 70iterations 0.1399627 3.289429 at 80iterations 7.7676199E-02 1.756214 at 90iterations 4.2779900E-02 1.027762 at 100iterations 2.3746027E-02 0.5413933 at 110iterations 1.3133411E-02 0.2719898 at 120iterations 7.2624912E-03 0.1540394 at 130iterations 4.0272279E-03 9.9311829E-02 at 140iterations 2.2353823E-03 4.9621582E-02 at 150iterations 1.2442558E-03 2.6702881E-02 at 160iterations 6.9595338E-04 1.5658140E-02 at 170iterations 3.9518747E-04 9.0160370E-03 at 180iterations finished qdiffx linear iterations at : 19:33:56 total time elapsed so far: 13.77000 # loops : 180 mean,max change (kT/e) : 3.9518747E-04 9.0160370E-03 energy calculations done at 13.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.89000 DelPhi exited at 19:33:56 13.896u 0.295s 0:14.80 95.8% 0+0k 0+0io 0pf+0w