Mon Oct 10 10:31:29 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 10:31:29 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 = 2883 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5546122 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): 18.05900 82.24800 ymin,ymax (A): 30.76000 89.24700 zmin,zma (A): -1.948000 50.56900 x,y,z range (A): 64.18900 58.48700 52.51700 scale (grids/A): 0.5546122 object centre (A): 50.15350 60.00350 24.31050 number of atom coordinates read : 2883 total number of charged atoms : 2731 net assigned charge : 6.000013 assigned positive charge : 421.9889 centred at (gu) : 87.92387 88.59399 86.79276 assigned negative charge : -415.9893 centred at (gu) : 87.81727 88.56790 86.73020 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6087 nv = 96 ne = 84 npr = 55517 no. pairs analyzed = 55517 no. exposed pairs = 4244 no. arc points = 30722 no. surface atoms = 1411 nbur = 1472 mkacc time = 0.1300000 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= 299 mr = 2798 m= 0 mr = 11 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3577 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2965 ## 358 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7651 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7933511E-11 4.9995136E-10 midg,1,midg; midg,igrid,midg 4.6483803E-10 5.5151339E-10 1,midg,midg; igrid,midg,midg -6.0776173E-10 8.6881757E-10 gauss-seidel spectral radius is 0.9832427 estimated iterations to convergence 64 setup time was (sec) 0.5900000 now iterating at: 10:31:30 rms-change max change #iterations 7.8096367E-02 16.24749 at 10iterations 5.3247744E-03 0.8993683 at 20iterations 3.8137360E-04 5.8250427E-02 at 30iterations 3.3452001E-05 5.2614212E-03 at 40iterations 4.9596765E-06 5.8746338E-04 at 50iterations finished qdiffx linear iterations at : 10:31:33 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 4.9596765E-06 5.8746338E-04 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 10:31:33 3.569u 0.191s 0:04.03 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 Mon Oct 10 2011 at 10:31:33 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 = 2883 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.663836 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): 18.05900 82.24800 ymin,ymax (A): 30.76000 89.24700 zmin,zma (A): -1.948000 50.56900 x,y,z range (A): 64.18900 58.48700 52.51700 scale (grids/A): 1.663836 object centre (A): 50.15350 60.00350 24.31050 number of atom coordinates read : 2883 total number of charged atoms : 2731 net assigned charge : 6.000013 assigned positive charge : 421.9889 centred at (gu) : 83.77086 85.78146 80.37772 assigned negative charge : -415.9893 centred at (gu) : 83.45158 85.70323 80.19026 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 66074 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30722 grid for indexing accessible points = 1.400000 m= 19909 mr = 41690 m= 2302 mr = 12576 m= 76 mr = 1002 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 33088 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 339 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 21046 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) : 0.5546122 object centre at (A) : 50.15350 60.00350 24.31050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0490797E-04 4.4433638E-03 midg,1,midg; midg,igrid,midg 4.4616293E-03 1.3211176E-02 1,midg,midg; igrid,midg,midg -1.7609715E-02 -9.0010082E-03 gauss-seidel spectral radius is 0.9982542 estimated iterations to convergence 190 setup time was (sec) 0.8200000 now iterating at: 10:31:34 rms-change max change #iterations 3.322487 170.8371 at 10iterations 1.403749 63.23736 at 20iterations 0.5912678 20.59671 at 30iterations 0.2505077 8.869232 at 40iterations 0.1057989 3.737036 at 50iterations 4.4608768E-02 1.759736 at 60iterations 1.8834958E-02 0.6678052 at 70iterations 7.9786228E-03 0.2913861 at 80iterations 3.3756716E-03 0.1230602 at 90iterations 1.4317025E-03 4.9552917E-02 at 100iterations 6.0655485E-04 2.0513535E-02 at 110iterations 2.5686255E-04 1.0910034E-02 at 120iterations finished qdiffx linear iterations at : 10:31:41 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 2.5686255E-04 1.0910034E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 10:31:42 7.912u 0.222s 0:08.49 95.7% 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 10:31:42 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 = 2883 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: 2.495755 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): 18.05900 82.24800 ymin,ymax (A): 30.76000 89.24700 zmin,zma (A): -1.948000 50.56900 x,y,z range (A): 64.18900 58.48700 52.51700 scale (grids/A): 2.495755 object centre (A): 50.15350 60.00350 24.31050 number of atom coordinates read : 2883 total number of charged atoms : 2731 net assigned charge : 6.000013 assigned positive charge : 421.9889 centred at (gu) : 80.65619 83.67206 75.56648 assigned negative charge : -415.9893 centred at (gu) : 80.17721 83.55480 75.28525 start vw surface at 0.1500000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 153711 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30722 grid for indexing accessible points = 1.400000 m= 67986 mr = 103371 m= 19885 mr = 51120 m= 3449 mr = 13952 m= 291 mr = 2050 m= 9 mr = 132 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 74706 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 21828 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) : 1.663836 object centre at (A) : 50.15350 60.00350 24.31050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6232777E-02 5.2180056E-02 midg,1,midg; midg,igrid,midg 2.1404641E-02 0.1922433 1,midg,midg; igrid,midg,midg -0.4969373 -0.3081685 gauss-seidel spectral radius is 0.9991636 estimated iterations to convergence 273 setup time was (sec) 1.560000 now iterating at: 10:31:44 rms-change max change #iterations 8.805587 285.2003 at 10iterations 5.093189 152.7339 at 20iterations 2.916216 95.04771 at 30iterations 1.651549 58.20101 at 40iterations 0.9337731 27.49007 at 50iterations 0.5227953 15.53056 at 60iterations 0.2934383 9.475873 at 70iterations 0.1637684 4.230989 at 80iterations 9.1338798E-02 3.291272 at 90iterations 5.0929509E-02 1.226497 at 100iterations 2.8366994E-02 0.7194958 at 110iterations 1.5747663E-02 0.4000447 at 120iterations 8.7986840E-03 0.1928215 at 130iterations 4.8771957E-03 0.1192894 at 140iterations 2.7035866E-03 5.9002399E-02 at 150iterations 1.5045888E-03 3.2577038E-02 at 160iterations 8.3638937E-04 2.0622253E-02 at 170iterations 4.6323502E-04 1.0709286E-02 at 180iterations finished qdiffx linear iterations at : 10:31:56 total time elapsed so far: 13.73000 # loops : 180 mean,max change (kT/e) : 4.6323502E-04 1.0709286E-02 energy calculations done at 13.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.92000 DelPhi exited at 10:31:56 13.919u 0.237s 0:14.47 97.7% 0+0k 0+0io 0pf+0w