Sun Oct 9 11:59:55 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 Sun Oct 9 2011 at 11:59:55 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2414 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: 0.6775919 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): -6.626000 44.59300 ymin,ymax (A): -14.34300 38.19600 zmin,zma (A): 2.453000 44.90500 x,y,z range (A): 51.21900 52.53900 42.45200 scale (grids/A): 0.6775919 object centre (A): 18.98350 11.92650 23.67900 number of atom coordinates read : 2414 total number of charged atoms : 2272 net assigned charge : 4.500025 assigned positive charge : 368.7480 centred at (gu) : 89.75906 90.90607 90.51187 assigned negative charge : -364.2485 centred at (gu) : 89.73375 91.06787 90.59812 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7476 nv = 96 ne = 84 npr = 48317 no. pairs analyzed = 48317 no. exposed pairs = 3036 no. arc points = 21617 no. surface atoms = 1013 nbur = 1401 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 443 mr = 4100 m= 2 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.1900000 number of dielectric boundary points 3749 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2147 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8708 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9195832E-08 -6.9924506E-09 midg,1,midg; midg,igrid,midg 5.3792171E-08 -3.4657514E-08 1,midg,midg; igrid,midg,midg 1.2102872E-08 2.4908072E-08 gauss-seidel spectral radius is 0.9886902 estimated iterations to convergence 77 setup time was (sec) 0.3800000 now iterating at: 11:59:55 rms-change max change #iterations 0.1753709 23.94019 at 10iterations 2.0101128E-02 2.707385 at 20iterations 2.7680015E-03 0.4119949 at 30iterations 5.9751363E-04 9.6023560E-02 at 40iterations 1.8869962E-04 3.0132294E-02 at 50iterations finished qdiffx linear iterations at : 11:59:58 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 1.8869962E-04 3.0132294E-02 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 11:59:59 3.381u 0.189s 0:03.85 92.4% 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 11:59:59 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 = 2414 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: 2.032776 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): -6.626000 44.59300 ymin,ymax (A): -14.34300 38.19600 zmin,zma (A): 2.453000 44.90500 x,y,z range (A): 51.21900 52.53900 42.45200 scale (grids/A): 2.032776 object centre (A): 18.98350 11.92650 23.67900 number of atom coordinates read : 2414 total number of charged atoms : 2272 net assigned charge : 4.500025 assigned positive charge : 368.7480 centred at (gu) : 89.27646 92.71796 91.53503 assigned negative charge : -364.2485 centred at (gu) : 89.20110 93.20335 91.79409 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79453 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21617 grid for indexing accessible points = 1.400000 m= 30367 mr = 55042 m= 5233 mr = 22487 m= 431 mr = 3292 m= 8 mr = 212 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1145 time to turn everything in is 0.4000000 number of dielectric boundary points 34459 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 128 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 18021 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) : 0.6775919 object centre at (A) : 18.98350 11.92650 23.67900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8307959E-02 8.7112179E-03 midg,1,midg; midg,igrid,midg 1.2117945E-02 -6.4568035E-02 1,midg,midg; igrid,midg,midg 3.6483124E-02 4.1752658E-03 gauss-seidel spectral radius is 0.9987808 estimated iterations to convergence 227 setup time was (sec) 0.6200000 now iterating at: 12:00:00 rms-change max change #iterations 4.616289 208.9589 at 10iterations 2.233879 88.24303 at 20iterations 1.090617 35.35356 at 30iterations 0.5342226 17.43704 at 40iterations 0.2605173 7.846915 at 50iterations 0.1268933 3.751266 at 60iterations 6.2463269E-02 2.004600 at 70iterations 3.0520668E-02 0.8837996 at 80iterations 1.5129553E-02 0.4861145 at 90iterations 7.5778901E-03 0.2531729 at 100iterations 3.8521681E-03 0.1263580 at 110iterations 2.0365587E-03 7.4619293E-02 at 120iterations finished qdiffx linear iterations at : 12:00:07 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 2.0365587E-03 7.4619293E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 12:00:07 7.928u 0.212s 0:08.41 96.6% 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 Sun Oct 9 2011 at 12:00:07 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 = 2414 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: 3.049163 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): -6.626000 44.59300 ymin,ymax (A): -14.34300 38.19600 zmin,zma (A): 2.453000 44.90500 x,y,z range (A): 51.21900 52.53900 42.45200 scale (grids/A): 3.049163 object centre (A): 18.98350 11.92650 23.67900 number of atom coordinates read : 2414 total number of charged atoms : 2272 net assigned charge : 4.500025 assigned positive charge : 368.7480 centred at (gu) : 88.91459 94.07666 92.30239 assigned negative charge : -364.2485 centred at (gu) : 88.80158 94.80499 92.69114 start vw surface at 0.1000000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 183079 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21617 grid for indexing accessible points = 1.400000 m= 96068 mr = 132675 m= 36826 mr = 79000 m= 9621 mr = 29494 m= 1749 mr = 7256 m= 183 mr = 1262 m= 2 mr = 120 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 4216 time to turn everything in is 1.050000 number of dielectric boundary points 77721 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 18176 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) : 2.032776 object centre at (A) : 18.98350 11.92650 23.67900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4197872 -2.3091275E-02 midg,1,midg; midg,igrid,midg 0.2605405 -0.7659259 1,midg,midg; igrid,midg,midg 0.3934593 -0.1657497 gauss-seidel spectral radius is 0.9992871 estimated iterations to convergence 296 setup time was (sec) 1.290000 now iterating at: 12:00:09 rms-change max change #iterations 10.58649 494.9829 at 10iterations 6.246232 121.4994 at 20iterations 3.680854 77.70306 at 30iterations 2.165595 41.21296 at 40iterations 1.267547 24.87619 at 50iterations 0.7406594 15.03978 at 60iterations 0.4336747 8.026648 at 70iterations 0.2539317 4.499396 at 80iterations 0.1483382 2.458784 at 90iterations 8.6575419E-02 1.511106 at 100iterations 5.0612666E-02 0.8842125 at 110iterations 2.9716864E-02 0.6100769 at 120iterations 1.7602969E-02 0.3230448 at 130iterations 1.0609672E-02 0.2337494 at 140iterations 6.5726526E-03 0.1223946 at 150iterations 4.2620855E-03 8.6902618E-02 at 160iterations 2.9344200E-03 6.2301636E-02 at 170iterations 2.1451295E-03 4.6154022E-02 at 180iterations finished qdiffx linear iterations at : 12:00:20 total time elapsed so far: 12.82000 # loops : 180 mean,max change (kT/e) : 2.1451295E-03 4.6154022E-02 energy calculations done at 12.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.95000 DelPhi exited at 12:00:21 12.952u 0.205s 0:13.43 97.9% 0+0k 0+0io 0pf+0w