Tue Oct 11 06:02:19 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 06:02:19 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 = 2327 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7032099 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): 25.73400 72.08400 ymin,ymax (A): -18.99700 31.62800 zmin,zma (A): 3.910000 46.22100 x,y,z range (A): 46.35000 50.62500 42.31100 scale (grids/A): 0.7032099 object centre (A): 48.90900 6.315500 25.06550 number of atom coordinates read : 2327 total number of charged atoms : 2002 net assigned charge : 6.500009 assigned positive charge : 325.3439 centred at (gu) : 89.26463 90.24738 90.36912 assigned negative charge : -318.8441 centred at (gu) : 89.39003 90.20084 90.45320 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7149 nv = 96 ne = 84 npr = 42736 no. pairs analyzed = 42736 no. exposed pairs = 2603 no. arc points = 17594 no. surface atoms = 889 nbur = 1438 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 484 mr = 4082 m= 2 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3459 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1603 ## 147 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 7922 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.1532363E-08 1.0852788E-08 midg,1,midg; midg,igrid,midg 2.6569891E-08 7.3991870E-08 1,midg,midg; igrid,midg,midg 1.2263105E-07 -7.4710291E-09 gauss-seidel spectral radius is 0.9894634 estimated iterations to convergence 79 setup time was (sec) 0.3500000 now iterating at: 06:02:20 rms-change max change #iterations 0.1950124 32.76609 at 10iterations 2.4231112E-02 3.228324 at 20iterations 3.3230814E-03 0.4457626 at 30iterations 6.2707870E-04 7.5344086E-02 at 40iterations 1.7872931E-04 2.0343781E-02 at 50iterations finished qdiffx linear iterations at : 06:02:23 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.7872931E-04 2.0343781E-02 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 06:02:23 3.320u 0.193s 0:04.02 87.3% 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 06:02:23 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 = 2327 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.109630 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): 25.73400 72.08400 ymin,ymax (A): -18.99700 31.62800 zmin,zma (A): 3.910000 46.22100 x,y,z range (A): 46.35000 50.62500 42.31100 scale (grids/A): 2.109630 object centre (A): 48.90900 6.315500 25.06550 number of atom coordinates read : 2327 total number of charged atoms : 2002 net assigned charge : 6.500009 assigned positive charge : 325.3439 centred at (gu) : 87.79383 90.74213 91.10744 assigned negative charge : -318.8441 centred at (gu) : 88.17014 90.60258 91.35978 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 75543 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17594 grid for indexing accessible points = 1.400000 m= 30745 mr = 53839 m= 5949 mr = 23288 m= 560 mr = 4037 m= 20 mr = 282 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 31371 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 15872 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) : 0.7032099 object centre at (A) : 48.90900 6.315500 25.06550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1076865E-02 2.6964860E-02 midg,1,midg; midg,igrid,midg 4.7881924E-02 2.8624605E-02 1,midg,midg; igrid,midg,midg 4.1920155E-02 -4.3416064E-02 gauss-seidel spectral radius is 0.9988223 estimated iterations to convergence 231 setup time was (sec) 0.6000000 now iterating at: 06:02:24 rms-change max change #iterations 4.609648 183.6506 at 10iterations 2.275000 81.34145 at 20iterations 1.123588 33.94938 at 30iterations 0.5582377 19.18564 at 40iterations 0.2766977 8.717066 at 50iterations 0.1371168 4.379475 at 60iterations 6.7916535E-02 1.947833 at 70iterations 3.3664290E-02 1.014289 at 80iterations 1.6829118E-02 0.4877391 at 90iterations 8.3968025E-03 0.2619047 at 100iterations 4.2410381E-03 0.1308949 at 110iterations 2.1964845E-03 6.9856644E-02 at 120iterations finished qdiffx linear iterations at : 06:02:31 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 2.1964845E-03 6.9856644E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 06:02:32 7.809u 0.211s 0:08.41 95.2% 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 Tue Oct 11 2011 at 06:02:32 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 = 2327 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.164444 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): 25.73400 72.08400 ymin,ymax (A): -18.99700 31.62800 zmin,zma (A): 3.910000 46.22100 x,y,z range (A): 46.35000 50.62500 42.31100 scale (grids/A): 3.164444 object centre (A): 48.90900 6.315500 25.06550 number of atom coordinates read : 2327 total number of charged atoms : 2002 net assigned charge : 6.500009 assigned positive charge : 325.3439 centred at (gu) : 86.69061 91.11330 91.66113 assigned negative charge : -318.8441 centred at (gu) : 87.25523 90.90378 92.03960 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 174004 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17594 grid for indexing accessible points = 1.400000 m= 95349 mr = 129455 m= 39075 mr = 79363 m= 11186 mr = 32131 m= 2235 mr = 8756 m= 290 mr = 1589 m= 16 mr = 183 m= 2 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.180000 number of dielectric boundary points 70676 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 16016 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) : 2.109630 object centre at (A) : 48.90900 6.315500 25.06550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1217208 0.2340128 midg,1,midg; midg,igrid,midg 0.3710097 0.1287107 1,midg,midg; igrid,midg,midg 0.4203812 -0.5392012 gauss-seidel spectral radius is 0.9992957 estimated iterations to convergence 297 setup time was (sec) 1.410000 now iterating at: 06:02:33 rms-change max change #iterations 10.34932 469.0214 at 10iterations 6.142288 141.9304 at 20iterations 3.634140 72.67667 at 30iterations 2.146804 42.80104 at 40iterations 1.266052 25.84179 at 50iterations 0.7454724 13.91010 at 60iterations 0.4379909 7.539726 at 70iterations 0.2565509 4.569480 at 80iterations 0.1506246 2.639652 at 90iterations 8.8355497E-02 1.606853 at 100iterations 5.1946834E-02 0.9414406 at 110iterations 3.0488530E-02 0.5566084 at 120iterations 1.7975427E-02 0.3321257 at 130iterations 1.0701843E-02 0.1961126 at 140iterations 6.4652893E-03 0.1213589 at 150iterations 3.9884886E-03 7.8330994E-02 at 160iterations 2.5717241E-03 4.7113419E-02 at 170iterations 1.7539514E-03 3.5972595E-02 at 180iterations finished qdiffx linear iterations at : 06:02:45 total time elapsed so far: 12.76000 # loops : 180 mean,max change (kT/e) : 1.7539514E-03 3.5972595E-02 energy calculations done at 12.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 06:02:46 12.907u 0.205s 0:13.85 94.5% 0+0k 0+0io 0pf+0w