Tue Oct 11 04:30:25 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 Tue Oct 11 2011 at 04:30:25 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 = 2721 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: 0.6415686 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): -11.94100 37.04400 ymin,ymax (A): -25.92900 22.39700 zmin,zma (A): -10.08300 45.40600 x,y,z range (A): 48.98500 48.32600 55.48900 scale (grids/A): 0.6415686 object centre (A): 12.55150 -1.766000 17.66150 number of atom coordinates read : 2721 total number of charged atoms : 2573 net assigned charge : 3.500013 assigned positive charge : 412.1927 centred at (gu) : 90.19365 90.44688 91.86778 assigned negative charge : -408.6933 centred at (gu) : 89.93890 90.25214 91.82542 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7356 nv = 96 ne = 84 npr = 56173 no. pairs analyzed = 56173 no. exposed pairs = 3247 no. arc points = 22706 no. surface atoms = 1105 nbur = 1616 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 379 mr = 4133 m= 0 mr = 37 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3565 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2282 ## 234 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8955 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6404147E-10 1.5608954E-08 midg,1,midg; midg,igrid,midg -1.8429839E-08 3.2416256E-08 1,midg,midg; igrid,midg,midg -2.7205504E-08 3.8302510E-08 gauss-seidel spectral radius is 0.9874187 estimated iterations to convergence 73 setup time was (sec) 0.4100000 now iterating at: 04:30:26 rms-change max change #iterations 0.1517275 19.58576 at 10iterations 1.5407562E-02 2.077444 at 20iterations 1.5349627E-03 0.2085381 at 30iterations 1.5517142E-04 2.1625519E-02 at 40iterations 1.5853071E-05 2.6025772E-03 at 50iterations finished qdiffx linear iterations at : 04:30:29 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 1.5853071E-05 2.6025772E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 04:30:29 3.457u 0.173s 0:04.13 87.6% 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 Tue Oct 11 2011 at 04:30:29 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 = 2721 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: 1.924706 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): -11.94100 37.04400 ymin,ymax (A): -25.92900 22.39700 zmin,zma (A): -10.08300 45.40600 x,y,z range (A): 48.98500 48.32600 55.48900 scale (grids/A): 1.924706 object centre (A): 12.55150 -1.766000 17.66150 number of atom coordinates read : 2721 total number of charged atoms : 2573 net assigned charge : 3.500013 assigned positive charge : 412.1927 centred at (gu) : 90.58023 91.33975 95.60268 assigned negative charge : -408.6933 centred at (gu) : 89.81621 90.75600 95.47601 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79797 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22706 grid for indexing accessible points = 1.400000 m= 28947 mr = 56278 m= 4249 mr = 21463 m= 209 mr = 2609 m= 2 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 857 time to turn everything in is 0.4000000 number of dielectric boundary points 32806 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 20249 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) : 0.6415686 object centre at (A) : 12.55150 -1.766000 17.66150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5200540E-02 1.1631717E-02 midg,1,midg; midg,igrid,midg -1.5107122E-02 2.9992701E-02 1,midg,midg; igrid,midg,midg -1.2323305E-02 5.2842736E-02 gauss-seidel spectral radius is 0.9986708 estimated iterations to convergence 217 setup time was (sec) 0.6200000 now iterating at: 04:30:30 rms-change max change #iterations 4.427989 171.3089 at 10iterations 2.093904 68.19209 at 20iterations 0.9933434 31.24477 at 30iterations 0.4721827 14.13567 at 40iterations 0.2233216 6.374657 at 50iterations 0.1055930 3.220940 at 60iterations 5.0250255E-02 1.592804 at 70iterations 2.3835139E-02 0.7305827 at 80iterations 1.1261069E-02 0.3587074 at 90iterations 5.3506615E-03 0.1556454 at 100iterations 2.5388799E-03 7.5395584E-02 at 110iterations 1.1997123E-03 3.9113998E-02 at 120iterations finished qdiffx linear iterations at : 04:30:37 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 1.1997123E-03 3.9113998E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 04:30:38 7.931u 0.205s 0:08.62 94.3% 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 Tue Oct 11 2011 at 04:30:38 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2721 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: 2.887058 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): -11.94100 37.04400 ymin,ymax (A): -25.92900 22.39700 zmin,zma (A): -10.08300 45.40600 x,y,z range (A): 48.98500 48.32600 55.48900 scale (grids/A): 2.887058 object centre (A): 12.55150 -1.766000 17.66150 number of atom coordinates read : 2721 total number of charged atoms : 2573 net assigned charge : 3.500013 assigned positive charge : 412.1927 centred at (gu) : 90.87047 92.00966 98.40391 assigned negative charge : -408.6933 centred at (gu) : 89.72444 91.13400 98.21401 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 184516 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22706 grid for indexing accessible points = 1.400000 m= 94728 mr = 136148 m= 33369 mr = 77981 m= 7485 mr = 26870 m= 935 mr = 5573 m= 53 mr = 568 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 2746 time to turn everything in is 1.020000 number of dielectric boundary points 73930 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 20584 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) : 1.924706 object centre at (A) : 12.55150 -1.766000 17.66150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5117477 0.3671451 midg,1,midg; midg,igrid,midg -0.1720004 0.3225589 1,midg,midg; igrid,midg,midg -0.1256904 0.4218110 gauss-seidel spectral radius is 0.9992645 estimated iterations to convergence 291 setup time was (sec) 1.260000 now iterating at: 04:30:39 rms-change max change #iterations 10.42842 355.0141 at 10iterations 6.105163 134.1534 at 20iterations 3.563486 67.76716 at 30iterations 2.077918 42.44805 at 40iterations 1.205351 22.90534 at 50iterations 0.6991653 12.01485 at 60iterations 0.4043458 8.047459 at 70iterations 0.2336891 4.040909 at 80iterations 0.1353778 2.476547 at 90iterations 7.7963017E-02 1.271703 at 100iterations 4.4987466E-02 0.8752861 at 110iterations 2.5945539E-02 0.4664221 at 120iterations 1.4986712E-02 0.2581024 at 130iterations 8.6675575E-03 0.1514263 at 140iterations 4.9997182E-03 8.8003159E-02 at 150iterations 2.8851973E-03 5.3782463E-02 at 160iterations 1.6705570E-03 2.9918671E-02 at 170iterations 9.6885307E-04 1.6784668E-02 at 180iterations finished qdiffx linear iterations at : 04:30:51 total time elapsed so far: 12.62000 # loops : 180 mean,max change (kT/e) : 9.6885307E-04 1.6784668E-02 energy calculations done at 12.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.75000 DelPhi exited at 04:30:51 12.749u 0.209s 0:13.24 97.7% 0+0k 0+0io 0pf+0w