Sun Oct 9 19:44:26 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 19:44:27 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: 347 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5425 !!! WARNING: HIR 341 has a net charge of 0.5140 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 0.5221396 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): 3.069000 67.20700 ymin,ymax (A): -9.254000 53.09600 zmin,zma (A): -1.850000 66.33100 x,y,z range (A): 64.13800 62.35000 68.18100 scale (grids/A): 0.5221396 object centre (A): 35.13800 21.92100 32.24050 number of atom coordinates read : 5425 total number of charged atoms : 5247 net assigned charge : 4.768030 assigned positive charge : 833.7132 centred at (gu) : 88.18328 89.37122 88.75739 assigned negative charge : -828.9511 centred at (gu) : 88.10174 89.37980 88.66459 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 9181 nv = 96 ne = 84 npr = 113140 no. pairs analyzed = 113140 no. exposed pairs = 6013 no. arc points = 41711 no. surface atoms = 2061 nbur = 3364 mkacc time = 0.2500000 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= 356 mr = 5191 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 4331 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4183 ## 575 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 12480 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.5966500E-10 4.1340595E-10 midg,1,midg; midg,igrid,midg 1.9622698E-10 7.1961319E-11 1,midg,midg; igrid,midg,midg -4.4681314E-10 3.2380010E-10 gauss-seidel spectral radius is 0.9812703 estimated iterations to convergence 60 setup time was (sec) 0.7100000 now iterating at: 19:44:27 rms-change max change #iterations 8.9859240E-02 15.93255 at 10iterations 9.7062048E-03 1.605591 at 20iterations 3.4720004E-03 0.6307030 at 30iterations 1.4818321E-03 0.2647362 at 40iterations 6.4269657E-04 0.1114731 at 50iterations finished qdiffx linear iterations at : 19:44:30 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 6.4269657E-04 0.1114731 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 19:44:30 3.286u 0.161s 0:03.73 92.2% 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 19:44:30 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: 347 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5425 !!! WARNING: HIR 341 has a net charge of 0.5140 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 1.566419 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): 3.069000 67.20700 ymin,ymax (A): -9.254000 53.09600 zmin,zma (A): -1.850000 66.33100 x,y,z range (A): 64.13800 62.35000 68.18100 scale (grids/A): 1.566419 object centre (A): 35.13800 21.92100 32.24050 number of atom coordinates read : 5425 total number of charged atoms : 5247 net assigned charge : 4.768030 assigned positive charge : 833.7132 centred at (gu) : 84.54790 88.11239 86.27071 assigned negative charge : -828.9511 centred at (gu) : 84.30486 88.13909 85.99352 start vw surface at 0.2100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 105438 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41711 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 31720 mr = 76386 m= 2947 mr = 22016 m= 61 mr = 1330 m= 0 mr = 6 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 40428 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 520 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 39566 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) : 0.5221396 object centre at (A) : 35.13800 21.92100 32.24050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9793047E-02 2.4540134E-02 midg,1,midg; midg,igrid,midg 1.7206494E-02 7.6369294E-03 1,midg,midg; igrid,midg,midg -1.3659829E-02 -7.6907303E-04 gauss-seidel spectral radius is 0.9982379 estimated iterations to convergence 189 setup time was (sec) 0.9500000 now iterating at: 19:44:31 rms-change max change #iterations 4.372971 161.7395 at 10iterations 1.851383 55.20658 at 20iterations 0.7818435 22.63431 at 30iterations 0.3323907 11.52518 at 40iterations 0.1414323 4.168282 at 50iterations 6.1125938E-02 1.975632 at 60iterations 2.7020523E-02 0.9080992 at 70iterations 1.2826061E-02 0.4112091 at 80iterations 6.8972022E-03 0.2282944 at 90iterations 4.2242580E-03 0.1537476 at 100iterations 2.8489027E-03 9.9731445E-02 at 110iterations 2.0169786E-03 6.8695068E-02 at 120iterations finished qdiffx linear iterations at : 19:44:37 total time elapsed so far: 6.970000 # loops : 120 mean,max change (kT/e) : 2.0169786E-03 6.8695068E-02 energy calculations done at 6.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.160000 DelPhi exited at 19:44:38 7.166u 0.174s 0:07.61 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 19:44:38 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: 347 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5425 !!! WARNING: HIR 341 has a net charge of 0.5140 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.349628 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): 3.069000 67.20700 ymin,ymax (A): -9.254000 53.09600 zmin,zma (A): -1.850000 66.33100 x,y,z range (A): 64.13800 62.35000 68.18100 scale (grids/A): 2.349628 object centre (A): 35.13800 21.92100 32.24050 number of atom coordinates read : 5425 total number of charged atoms : 5247 net assigned charge : 4.768030 assigned positive charge : 833.7132 centred at (gu) : 81.82157 87.16810 84.40565 assigned negative charge : -828.9511 centred at (gu) : 81.45740 87.20871 83.99026 start vw surface at 0.2200000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 246271 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41711 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 112990 mr = 186688 m= 30288 mr = 90728 m= 4303 mr = 22455 m= 261 mr = 2738 m= 3 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.670000 number of dielectric boundary points 91396 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 52 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 41861 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) : 1.566419 object centre at (A) : 35.13800 21.92100 32.24050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4650713 0.7070415 midg,1,midg; midg,igrid,midg 0.3042469 5.8521230E-02 1,midg,midg; igrid,midg,midg -0.3422202 -4.7683003E-03 gauss-seidel spectral radius is 0.9991976 estimated iterations to convergence 279 setup time was (sec) 1.950000 now iterating at: 19:44:40 rms-change max change #iterations 11.42059 264.5664 at 10iterations 6.561479 144.4527 at 20iterations 3.752570 80.97791 at 30iterations 2.130786 41.49255 at 40iterations 1.209742 25.18488 at 50iterations 0.6847552 11.61359 at 60iterations 0.3870893 6.961937 at 70iterations 0.2191747 3.898492 at 80iterations 0.1235836 2.178940 at 90iterations 7.0107676E-02 1.163754 at 100iterations 3.9926495E-02 0.8181000 at 110iterations 2.2910681E-02 0.4268303 at 120iterations 1.3517433E-02 0.2587280 at 130iterations 8.2285041E-03 0.1718559 at 140iterations 5.2750977E-03 0.1107101 at 150iterations 3.6054060E-03 7.5576782E-02 at 160iterations 2.6294952E-03 5.4443359E-02 at 170iterations 2.0128735E-03 4.3380737E-02 at 180iterations finished qdiffx linear iterations at : 19:44:50 total time elapsed so far: 11.55000 # loops : 180 mean,max change (kT/e) : 2.0128735E-03 4.3380737E-02 energy calculations done at 11.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.72000 DelPhi exited at 19:44:50 11.724u 0.175s 0:12.18 97.6% 0+0k 0+0io 0pf+0w