Sun Oct 9 13:20:50 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 13:20:50 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2393 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 0.6788452 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): -6.971000 44.56600 ymin,ymax (A): 22.15500 74.59700 zmin,zma (A): 40.55900 84.33200 x,y,z range (A): 51.53700 52.44200 43.77300 scale (grids/A): 0.6788452 object centre (A): 18.79750 48.37600 62.44550 number of atom coordinates read : 2393 total number of charged atoms : 2247 net assigned charge : 3.406025 assigned positive charge : 367.4511 centred at (gu) : 89.81757 90.76585 90.78301 assigned negative charge : -364.0456 centred at (gu) : 89.80678 90.93816 90.86796 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7421 nv = 96 ne = 84 npr = 48314 no. pairs analyzed = 48314 no. exposed pairs = 3037 no. arc points = 21163 no. surface atoms = 1015 nbur = 1378 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 472 mr = 4088 m= 4 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3748 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2046 ## 195 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8531 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4058917E-08 -1.2480458E-08 midg,1,midg; midg,igrid,midg 5.5711908E-08 -4.3631893E-08 1,midg,midg; igrid,midg,midg 1.2150626E-08 1.7487899E-08 gauss-seidel spectral radius is 0.9887287 estimated iterations to convergence 77 setup time was (sec) 0.5900000 now iterating at: 13:20:51 rms-change max change #iterations 0.1871783 27.61926 at 10iterations 2.1621956E-02 2.843024 at 20iterations 2.9301238E-03 0.4139099 at 30iterations 6.5414177E-04 0.1023636 at 40iterations 2.0796603E-04 3.3050537E-02 at 50iterations finished qdiffx linear iterations at : 13:20:54 total time elapsed so far: 3.510000 # loops : 50 mean,max change (kT/e) : 2.0796603E-04 3.3050537E-02 energy calculations done at 3.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.700000 DelPhi exited at 13:20:55 3.706u 0.211s 0:04.20 93.0% 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 13:20:55 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2393 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 2.036536 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): -6.971000 44.56600 ymin,ymax (A): 22.15500 74.59700 zmin,zma (A): 40.55900 84.33200 x,y,z range (A): 51.53700 52.44200 43.77300 scale (grids/A): 2.036536 object centre (A): 18.79750 48.37600 62.44550 number of atom coordinates read : 2393 total number of charged atoms : 2247 net assigned charge : 3.406025 assigned positive charge : 367.4511 centred at (gu) : 89.45208 92.29730 92.34865 assigned negative charge : -364.0456 centred at (gu) : 89.41997 92.81422 92.60376 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 78210 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21163 grid for indexing accessible points = 1.400000 m= 29810 mr = 53775 m= 5388 mr = 21985 m= 473 mr = 3443 m= 6 mr = 241 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 300 time to turn everything in is 0.6100000 number of dielectric boundary points 34443 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 17790 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) : 0.6788452 object centre at (A) : 18.79750 48.37600 62.44550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6465348E-02 -6.8988273E-04 midg,1,midg; midg,igrid,midg 1.4760401E-02 -6.4612366E-02 1,midg,midg; igrid,midg,midg 4.0967196E-02 7.7562132E-03 gauss-seidel spectral radius is 0.9987812 estimated iterations to convergence 227 setup time was (sec) 0.9300000 now iterating at: 13:20:56 rms-change max change #iterations 4.685289 268.0931 at 10iterations 2.270648 72.51879 at 20iterations 1.110291 40.76459 at 30iterations 0.5435752 19.11107 at 40iterations 0.2656425 8.317982 at 50iterations 0.1295290 4.140155 at 60iterations 6.3504726E-02 1.876328 at 70iterations 3.1210786E-02 0.9703598 at 80iterations 1.5403147E-02 0.4890327 at 90iterations 7.6505765E-03 0.2240028 at 100iterations 3.8697186E-03 0.1342049 at 110iterations 2.0278138E-03 6.5238953E-02 at 120iterations finished qdiffx linear iterations at : 13:21:03 total time elapsed so far: 8.180000 # loops : 120 mean,max change (kT/e) : 2.0278138E-03 6.5238953E-02 energy calculations done at 8.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.360000 DelPhi exited at 13:21:04 8.366u 0.287s 0:08.95 96.5% 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 13:21:04 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2393 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 3.054803 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): -6.971000 44.56600 ymin,ymax (A): 22.15500 74.59700 zmin,zma (A): 40.55900 84.33200 x,y,z range (A): 51.53700 52.44200 43.77300 scale (grids/A): 3.054803 object centre (A): 18.79750 48.37600 62.44550 number of atom coordinates read : 2393 total number of charged atoms : 2247 net assigned charge : 3.406025 assigned positive charge : 367.4511 centred at (gu) : 89.17802 93.44584 93.52277 assigned negative charge : -364.0456 centred at (gu) : 89.12998 94.22123 93.90559 start vw surface at 0.1500000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 180493 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21163 grid for indexing accessible points = 1.400000 m= 94070 mr = 130504 m= 36727 mr = 76697 m= 9857 mr = 29509 m= 1916 mr = 7431 m= 231 mr = 1389 m= 6 mr = 135 m= 0 mr = 0 time to grow re-entrant surface = 0.9399999 no. cavity mid-points inaccessible to solvent = 874 time to turn everything in is 1.590000 number of dielectric boundary points 77635 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 17976 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) : 2.036536 object centre at (A) : 18.79750 48.37600 62.44550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4567055 -0.1295231 midg,1,midg; midg,igrid,midg 0.3582627 -0.7005996 1,midg,midg; igrid,midg,midg 0.4442723 -0.1599775 gauss-seidel spectral radius is 0.9992875 estimated iterations to convergence 296 setup time was (sec) 1.940000 now iterating at: 13:21:06 rms-change max change #iterations 10.71782 423.0817 at 10iterations 6.330561 136.4021 at 20iterations 3.734143 82.11772 at 30iterations 2.196478 44.54731 at 40iterations 1.291769 22.87686 at 50iterations 0.7561917 14.82781 at 60iterations 0.4423110 7.954041 at 70iterations 0.2592010 4.901146 at 80iterations 0.1511342 2.861238 at 90iterations 8.8200860E-02 1.578152 at 100iterations 5.1698059E-02 0.8833466 at 110iterations 3.0341255E-02 0.5026913 at 120iterations 1.7930558E-02 0.3237944 at 130iterations 1.0680079E-02 0.2290802 at 140iterations 6.5524038E-03 0.1218801 at 150iterations 4.1723293E-03 8.8603973E-02 at 160iterations 2.8001061E-03 5.9482574E-02 at 170iterations 2.0002539E-03 4.7216415E-02 at 180iterations finished qdiffx linear iterations at : 13:21:18 total time elapsed so far: 14.04000 # loops : 180 mean,max change (kT/e) : 2.0002539E-03 4.7216415E-02 energy calculations done at 14.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.25000 DelPhi exited at 13:21:18 14.249u 0.286s 0:14.81 98.0% 0+0k 0+0io 0pf+0w