Sun Oct 9 06:04:12 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 06:04:12 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1866 !!! WARNING: HIR 132 has a net charge of 0.5140 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: 0.6452081 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): 18.89100 69.66600 ymin,ymax (A): 15.47000 70.64600 zmin,zma (A): 47.09200 93.26300 x,y,z range (A): 50.77500 55.17599 46.17100 scale (grids/A): 0.6452081 object centre (A): 44.27850 43.05800 70.17751 number of atom coordinates read : 1866 total number of charged atoms : 1724 net assigned charge : -8.985989 assigned positive charge : 290.2799 centred at (gu) : 89.89827 87.55762 88.72897 assigned negative charge : -299.2661 centred at (gu) : 90.11937 87.42464 89.03311 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5297 nv = 96 ne = 84 npr = 36793 no. pairs analyzed = 36793 no. exposed pairs = 2528 no. arc points = 18324 no. surface atoms = 847 nbur = 1019 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 270 mr = 2646 m= 0 mr = 26 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.2300000 number of dielectric boundary points 2895 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1710 ## 161 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 6109 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0295092E-08 -3.6175493E-08 midg,1,midg; midg,igrid,midg -4.8735732E-08 -1.2005261E-09 1,midg,midg; igrid,midg,midg 7.2851876E-09 -3.7491141E-08 gauss-seidel spectral radius is 0.9874951 estimated iterations to convergence 73 setup time was (sec) 0.4700000 now iterating at: 06:04:12 rms-change max change #iterations 0.1314666 25.56194 at 10iterations 1.2647809E-02 2.163103 at 20iterations 1.2842953E-03 0.2085075 at 30iterations 1.2862183E-04 2.3480415E-02 at 40iterations 1.2821316E-05 2.3956299E-03 at 50iterations finished qdiffx linear iterations at : 06:04:15 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.2821316E-05 2.3956299E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 06:04:15 3.360u 0.214s 0:03.83 93.2% 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 06:04:15 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1866 !!! WARNING: HIR 132 has a net charge of 0.5140 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: 1.935624 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): 18.89100 69.66600 ymin,ymax (A): 15.47000 70.64600 zmin,zma (A): 47.09200 93.26300 x,y,z range (A): 50.77500 55.17599 46.17100 scale (grids/A): 1.935624 object centre (A): 44.27850 43.05800 70.17751 number of atom coordinates read : 1866 total number of charged atoms : 1724 net assigned charge : -8.985989 assigned positive charge : 290.2799 centred at (gu) : 89.69447 82.67274 86.18702 assigned negative charge : -299.2661 centred at (gu) : 90.35809 82.27366 87.09932 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 56593 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18324 grid for indexing accessible points = 1.400000 m= 19161 mr = 36715 m= 2903 mr = 13582 m= 149 mr = 1704 m= 0 mr = 36 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 637 time to turn everything in is 0.4200000 number of dielectric boundary points 26769 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 108 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 13581 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) : 0.6452081 object centre at (A) : 44.27850 43.05800 70.17751 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9790894E-03 -3.8123567E-02 midg,1,midg; midg,igrid,midg -9.9374451E-02 -1.7008847E-02 1,midg,midg; igrid,midg,midg 2.5950609E-02 -4.6707626E-02 gauss-seidel spectral radius is 0.9986047 estimated iterations to convergence 212 setup time was (sec) 0.7100000 now iterating at: 06:04:16 rms-change max change #iterations 3.851619 206.9539 at 10iterations 1.782017 69.83987 at 20iterations 0.8250901 30.42580 at 30iterations 0.3819069 15.98050 at 40iterations 0.1769280 6.743124 at 50iterations 8.2050905E-02 2.890490 at 60iterations 3.7946992E-02 1.521699 at 70iterations 1.7602945E-02 0.6564732 at 80iterations 8.1476560E-03 0.2921982 at 90iterations 3.7826092E-03 0.1376495 at 100iterations 1.7456900E-03 6.5456152E-02 at 110iterations 8.1450038E-04 2.9075623E-02 at 120iterations finished qdiffx linear iterations at : 06:04:23 total time elapsed so far: 7.380000 # loops : 120 mean,max change (kT/e) : 8.1450038E-04 2.9075623E-02 energy calculations done at 7.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.550000 DelPhi exited at 06:04:24 7.550u 0.256s 0:08.16 95.5% 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 06:04:24 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1866 !!! WARNING: HIR 132 has a net charge of 0.5140 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: 2.903437 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): 18.89100 69.66600 ymin,ymax (A): 15.47000 70.64600 zmin,zma (A): 47.09200 93.26300 x,y,z range (A): 50.77500 55.17599 46.17100 scale (grids/A): 2.903437 object centre (A): 44.27850 43.05800 70.17751 number of atom coordinates read : 1866 total number of charged atoms : 1724 net assigned charge : -8.985989 assigned positive charge : 290.2799 centred at (gu) : 89.54176 79.00906 84.28060 assigned negative charge : -299.2661 centred at (gu) : 90.53705 78.41058 85.64890 start vw surface at 0.1300000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 130709 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18324 grid for indexing accessible points = 1.400000 m= 62626 mr = 89508 m= 21666 mr = 49933 m= 5096 mr = 16933 m= 654 mr = 3632 m= 26 mr = 411 m= 0 mr = 7 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 2000 time to turn everything in is 1.030000 number of dielectric boundary points 60353 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 13791 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) : 1.935624 object centre at (A) : 44.27850 43.05800 70.17751 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.6934011E-03 -0.4014912 midg,1,midg; midg,igrid,midg -0.9409384 -0.1235925 1,midg,midg; igrid,midg,midg 0.1480950 -0.7346039 gauss-seidel spectral radius is 0.9992397 estimated iterations to convergence 286 setup time was (sec) 1.350000 now iterating at: 06:04:25 rms-change max change #iterations 8.984088 431.5909 at 10iterations 5.197452 130.1438 at 20iterations 2.982471 65.56557 at 30iterations 1.709815 38.99387 at 40iterations 0.9756296 20.16275 at 50iterations 0.5573205 12.74163 at 60iterations 0.3184045 6.665016 at 70iterations 0.1809015 4.215324 at 80iterations 0.1032845 2.049557 at 90iterations 5.8741484E-02 1.137421 at 100iterations 3.3494797E-02 0.7424316 at 110iterations 1.9026779E-02 0.4298077 at 120iterations 1.0844994E-02 0.2337825 at 130iterations 6.1864387E-03 0.1307106 at 140iterations 3.5183299E-03 7.0719719E-02 at 150iterations 2.0049834E-03 4.5022488E-02 at 160iterations 1.1404628E-03 2.2651672E-02 at 170iterations 6.4973463E-04 1.3648033E-02 at 180iterations finished qdiffx linear iterations at : 06:04:36 total time elapsed so far: 12.07000 # loops : 180 mean,max change (kT/e) : 6.4973463E-04 1.3648033E-02 energy calculations done at 12.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.24000 DelPhi exited at 06:04:36 12.246u 0.259s 0:12.79 97.6% 0+0k 0+0io 0pf+0w