Sun Oct 9 10:14:51 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 10:14:51 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2876 !!! WARNING: HIR 213 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6115577 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): -6.708000 49.83500 ymin,ymax (A): -5.290000 45.41200 zmin,zma (A): -13.77000 44.44200 x,y,z range (A): 56.54300 50.70200 58.21200 scale (grids/A): 0.6115577 object centre (A): 21.56350 20.06100 15.33600 number of atom coordinates read : 2876 total number of charged atoms : 2792 net assigned charge : 1.4021963E-02 assigned positive charge : 429.4331 centred at (gu) : 89.71381 89.91849 91.10905 assigned negative charge : -429.4208 centred at (gu) : 89.72205 89.93256 91.13238 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7377 nv = 96 ne = 84 npr = 56148 no. pairs analyzed = 56148 no. exposed pairs = 4102 no. arc points = 28938 no. surface atoms = 1338 nbur = 1538 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 416 mr = 3611 m= 6 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 4161 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2873 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9154 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0554515E-09 -1.6994648E-09 midg,1,midg; midg,igrid,midg 8.4329066E-10 -7.7138057E-10 1,midg,midg; igrid,midg,midg 5.2749993E-10 -4.2215503E-10 gauss-seidel spectral radius is 0.9861957 estimated iterations to convergence 70 setup time was (sec) 0.5200000 now iterating at: 10:14:52 rms-change max change #iterations 0.1223340 19.79091 at 10iterations 1.1368535E-02 1.649239 at 20iterations 1.3477912E-03 0.1977158 at 30iterations 3.3849390E-04 5.4200172E-02 at 40iterations 1.1685629E-04 1.8768311E-02 at 50iterations finished qdiffx linear iterations at : 10:14:54 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 1.1685629E-04 1.8768311E-02 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 10:14:55 3.178u 0.130s 0:03.58 92.1% 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 10:14:55 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2876 !!! WARNING: HIR 213 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.834673 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): -6.708000 49.83500 ymin,ymax (A): -5.290000 45.41200 zmin,zma (A): -13.77000 44.44200 x,y,z range (A): 56.54300 50.70200 58.21200 scale (grids/A): 1.834673 object centre (A): 21.56350 20.06100 15.33600 number of atom coordinates read : 2876 total number of charged atoms : 2792 net assigned charge : 1.4021963E-02 assigned positive charge : 429.4331 centred at (gu) : 89.14089 89.75478 93.32633 assigned negative charge : -429.4208 centred at (gu) : 89.16611 89.79798 93.39713 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 79318 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28938 grid for indexing accessible points = 1.400000 m= 27441 mr = 52170 m= 4517 mr = 18472 m= 285 mr = 2329 m= 6 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 38542 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 21896 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) : 0.6115577 object centre at (A) : 21.56350 20.06100 15.33600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5519833E-03 -4.7097304E-03 midg,1,midg; midg,igrid,midg 1.3768354E-02 1.2440727E-02 1,midg,midg; igrid,midg,midg -5.8881245E-03 -6.5804897E-03 gauss-seidel spectral radius is 0.9985879 estimated iterations to convergence 211 setup time was (sec) 0.8500000 now iterating at: 10:14:56 rms-change max change #iterations 4.208215 193.5055 at 10iterations 1.937681 70.63292 at 20iterations 0.8911592 30.28349 at 30iterations 0.4127854 13.17946 at 40iterations 0.1907809 6.517408 at 50iterations 8.8155657E-02 2.848297 at 60iterations 4.0815927E-02 1.324862 at 70iterations 1.8901212E-02 0.5671959 at 80iterations 8.8313678E-03 0.2674294 at 90iterations 4.1784197E-03 0.1368752 at 100iterations 2.0296364E-03 7.8733444E-02 at 110iterations 1.0372774E-03 3.5778046E-02 at 120iterations finished qdiffx linear iterations at : 10:15:02 total time elapsed so far: 6.870000 # loops : 120 mean,max change (kT/e) : 1.0372774E-03 3.5778046E-02 energy calculations done at 6.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.050000 DelPhi exited at 10:15:02 7.048u 0.161s 0:07.48 96.2% 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 10:15:02 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2876 !!! WARNING: HIR 213 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.752010 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): -6.708000 49.83500 ymin,ymax (A): -5.290000 45.41200 zmin,zma (A): -13.77000 44.44200 x,y,z range (A): 56.54300 50.70200 58.21200 scale (grids/A): 2.752010 object centre (A): 21.56350 20.06100 15.33600 number of atom coordinates read : 2876 total number of charged atoms : 2792 net assigned charge : 1.4021963E-02 assigned positive charge : 429.4331 centred at (gu) : 88.71121 89.63184 94.98925 assigned negative charge : -429.4208 centred at (gu) : 88.74906 89.69703 95.09563 start vw surface at 0.1600000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 183407 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28938 grid for indexing accessible points = 1.400000 m= 88434 mr = 128069 m= 31467 mr = 68128 m= 7940 mr = 23453 m= 1065 mr = 5248 m= 63 mr = 498 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.390000 number of dielectric boundary points 86970 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 22331 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) : 1.834673 object centre at (A) : 21.56350 20.06100 15.33600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4491321E-02 -0.2599081 midg,1,midg; midg,igrid,midg 0.2700675 0.2563559 1,midg,midg; igrid,midg,midg -3.0607332E-02 -1.6301107E-02 gauss-seidel spectral radius is 0.9992668 estimated iterations to convergence 291 setup time was (sec) 1.680000 now iterating at: 10:15:04 rms-change max change #iterations 10.24766 283.0962 at 10iterations 6.162521 148.2816 at 20iterations 3.647882 81.70454 at 30iterations 2.151197 51.98445 at 40iterations 1.259946 27.69974 at 50iterations 0.7376841 14.18991 at 60iterations 0.4297307 8.809677 at 70iterations 0.2499481 4.416445 at 80iterations 0.1453486 2.954639 at 90iterations 8.4211610E-02 1.593313 at 100iterations 4.8859149E-02 0.8625908 at 110iterations 2.8270654E-02 0.5541916 at 120iterations 1.6383305E-02 0.2882385 at 130iterations 9.5048370E-03 0.1837502 at 140iterations 5.5186162E-03 0.1030515 at 150iterations 3.2249105E-03 6.0542107E-02 at 160iterations 1.9006915E-03 3.5484314E-02 at 170iterations 1.1375190E-03 2.1734238E-02 at 180iterations finished qdiffx linear iterations at : 10:15:14 total time elapsed so far: 11.76000 # loops : 180 mean,max change (kT/e) : 1.1375190E-03 2.1734238E-02 energy calculations done at 11.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.93000 DelPhi exited at 10:15:15 11.932u 0.172s 0:12.42 97.4% 0+0k 0+0io 0pf+0w