Sun Oct 9 16:20:41 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 16:20:41 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3145 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: 0.6225518 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): -19.08900 37.54800 ymin,ymax (A): 53.83300 106.4620 zmin,zma (A): -0.9809999 56.20300 x,y,z range (A): 56.63700 52.62900 57.18400 scale (grids/A): 0.6225518 object centre (A): 9.229500 80.14750 27.61100 number of atom coordinates read : 3145 total number of charged atoms : 3003 net assigned charge : -3.499985 assigned positive charge : 469.1908 centred at (gu) : 90.14582 90.10693 90.13472 assigned negative charge : -472.6922 centred at (gu) : 90.08467 90.05459 90.23037 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8095 nv = 96 ne = 84 npr = 64342 no. pairs analyzed = 64342 no. exposed pairs = 4056 no. arc points = 28663 no. surface atoms = 1356 nbur = 1789 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 410 mr = 4220 m= 4 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.2300000 number of dielectric boundary points 4232 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2836 ## 282 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9932 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0532796E-09 -1.1821330E-08 midg,1,midg; midg,igrid,midg -7.4575990E-09 1.5374312E-09 1,midg,midg; igrid,midg,midg -8.1474090E-09 2.3356959E-09 gauss-seidel spectral radius is 0.9866893 estimated iterations to convergence 71 setup time was (sec) 0.4300000 now iterating at: 16:20:41 rms-change max change #iterations 0.1443841 21.60040 at 10iterations 1.3423617E-02 1.858498 at 20iterations 1.3108412E-03 0.1572742 at 30iterations 1.6545862E-04 1.8455505E-02 at 40iterations 3.9012601E-05 4.1450262E-03 at 50iterations finished qdiffx linear iterations at : 16:20:44 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 3.9012601E-05 4.1450262E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 16:20:45 3.458u 0.169s 0:03.88 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 16:20:45 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3145 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: 1.867655 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): -19.08900 37.54800 ymin,ymax (A): 53.83300 106.4620 zmin,zma (A): -0.9809999 56.20300 x,y,z range (A): 56.63700 52.62900 57.18400 scale (grids/A): 1.867655 object centre (A): 9.229500 80.14750 27.61100 number of atom coordinates read : 3145 total number of charged atoms : 3003 net assigned charge : -3.499985 assigned positive charge : 469.1908 centred at (gu) : 90.43667 90.32007 90.40357 assigned negative charge : -472.6922 centred at (gu) : 90.25361 90.16332 90.69088 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 87658 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28663 grid for indexing accessible points = 1.400000 m= 30327 mr = 59394 m= 4872 mr = 21409 m= 263 mr = 2904 m= 7 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1770 time to turn everything in is 0.4200000 number of dielectric boundary points 39335 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 180 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 23535 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) : 0.6225518 object centre at (A) : 9.229500 80.14750 27.61100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1679107E-02 -1.5761334E-02 midg,1,midg; midg,igrid,midg -1.3654756E-02 -2.0423254E-02 1,midg,midg; igrid,midg,midg -3.0096255E-02 -2.1838505E-02 gauss-seidel spectral radius is 0.9986454 estimated iterations to convergence 215 setup time was (sec) 0.6500000 now iterating at: 16:20:46 rms-change max change #iterations 4.545393 160.5503 at 10iterations 2.122210 78.19402 at 20iterations 0.9942094 29.38616 at 30iterations 0.4680989 13.87171 at 40iterations 0.2198353 6.497833 at 50iterations 0.1029622 2.913302 at 60iterations 4.8387706E-02 1.444296 at 70iterations 2.2744793E-02 0.6491547 at 80iterations 1.0671666E-02 0.2882652 at 90iterations 5.0285710E-03 0.1518092 at 100iterations 2.3748234E-03 7.0353985E-02 at 110iterations 1.1230964E-03 3.7981987E-02 at 120iterations finished qdiffx linear iterations at : 16:20:53 total time elapsed so far: 7.880000 # loops : 120 mean,max change (kT/e) : 1.1230964E-03 3.7981987E-02 energy calculations done at 7.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.010000 DelPhi exited at 16:20:53 8.010u 0.195s 0:08.51 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 16:20:53 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3145 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: 2.801483 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): -19.08900 37.54800 ymin,ymax (A): 53.83300 106.4620 zmin,zma (A): -0.9809999 56.20300 x,y,z range (A): 56.63700 52.62900 57.18400 scale (grids/A): 2.801483 object centre (A): 9.229500 80.14750 27.61100 number of atom coordinates read : 3145 total number of charged atoms : 3003 net assigned charge : -3.499985 assigned positive charge : 469.1908 centred at (gu) : 90.65462 90.47977 90.60498 assigned negative charge : -472.6922 centred at (gu) : 90.38038 90.24486 91.03616 start vw surface at 0.1000000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 203089 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28663 grid for indexing accessible points = 1.400000 m= 97997 mr = 145153 m= 35278 mr = 77667 m= 8582 mr = 27634 m= 1100 mr = 6285 m= 48 mr = 716 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 5562 time to turn everything in is 1.110000 number of dielectric boundary points 88623 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 24023 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) : 1.867655 object centre at (A) : 9.229500 80.14750 27.61100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8884249 -0.1732675 midg,1,midg; midg,igrid,midg -0.1828958 -0.3947992 1,midg,midg; igrid,midg,midg -0.3092003 -0.3411255 gauss-seidel spectral radius is 0.9992858 estimated iterations to convergence 295 setup time was (sec) 1.350000 now iterating at: 16:20:55 rms-change max change #iterations 10.99566 359.4527 at 10iterations 6.594224 159.0990 at 20iterations 3.917739 96.31866 at 30iterations 2.313219 56.35632 at 40iterations 1.365732 27.54406 at 50iterations 0.8028255 16.20512 at 60iterations 0.4711170 9.235022 at 70iterations 0.2754060 5.323324 at 80iterations 0.1610780 3.085978 at 90iterations 9.4087295E-02 1.818653 at 100iterations 5.4879386E-02 1.006912 at 110iterations 3.1980451E-02 0.6486912 at 120iterations 1.8624173E-02 0.3973999 at 130iterations 1.0840113E-02 0.1902008 at 140iterations 6.3189082E-03 0.1100919 at 150iterations 3.6734291E-03 6.2934875E-02 at 160iterations 2.1431413E-03 3.7157059E-02 at 170iterations 1.2444076E-03 2.1961212E-02 at 180iterations finished qdiffx linear iterations at : 16:21:06 total time elapsed so far: 13.06000 # loops : 180 mean,max change (kT/e) : 1.2444076E-03 2.1961212E-02 energy calculations done at 13.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.19000 DelPhi exited at 16:21:07 13.187u 0.215s 0:13.66 98.0% 0+0k 0+0io 0pf+0w