Sun Oct 9 13:11:21 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 13:11:21 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 = 2356 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: 0.7021281 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): -6.052000 44.54800 ymin,ymax (A): -14.18600 36.51700 zmin,zma (A): 1.247000 45.52200 x,y,z range (A): 50.60000 50.70300 44.27500 scale (grids/A): 0.7021281 object centre (A): 19.24800 11.16550 23.38450 number of atom coordinates read : 2356 total number of charged atoms : 2216 net assigned charge : 4.500011 assigned positive charge : 358.3491 centred at (gu) : 89.44099 91.38841 90.95608 assigned negative charge : -353.8496 centred at (gu) : 89.43028 91.52362 91.01501 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 8171 nv = 96 ne = 84 npr = 46095 no. pairs analyzed = 46095 no. exposed pairs = 2995 no. arc points = 20915 no. surface atoms = 1005 nbur = 1351 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 527 mr = 4587 m= 2 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.1800000 number of dielectric boundary points 4012 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1965 ## 203 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8911 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.3067133E-08 6.0922374E-09 midg,1,midg; midg,igrid,midg 7.6974978E-08 -4.4710902E-08 1,midg,midg; igrid,midg,midg 3.2766660E-08 3.6057362E-08 gauss-seidel spectral radius is 0.9894621 estimated iterations to convergence 79 setup time was (sec) 0.3500000 now iterating at: 13:11:21 rms-change max change #iterations 0.2047055 35.81286 at 10iterations 2.5502410E-02 3.372978 at 20iterations 3.6246891E-03 0.4996815 at 30iterations 8.4794825E-04 0.1379967 at 40iterations 2.9962559E-04 4.9139023E-02 at 50iterations finished qdiffx linear iterations at : 13:11:24 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 2.9962559E-04 4.9139023E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 13:11:25 3.316u 0.199s 0:03.79 92.3% 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 Sun Oct 9 2011 at 13:11:25 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 = 2356 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: 2.106384 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): -6.052000 44.54800 ymin,ymax (A): -14.18600 36.51700 zmin,zma (A): 1.247000 45.52200 x,y,z range (A): 50.60000 50.70300 44.27500 scale (grids/A): 2.106384 object centre (A): 19.24800 11.16550 23.38450 number of atom coordinates read : 2356 total number of charged atoms : 2216 net assigned charge : 4.500011 assigned positive charge : 358.3491 centred at (gu) : 88.32267 94.16479 92.86790 assigned negative charge : -353.8496 centred at (gu) : 88.29059 94.57059 93.04487 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 85820 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20915 grid for indexing accessible points = 1.400000 m= 35211 mr = 59899 m= 6850 mr = 26956 m= 647 mr = 4593 m= 14 mr = 360 m= 0 mr = 4 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 514 time to turn everything in is 0.4300000 number of dielectric boundary points 36730 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 113 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 17607 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) : 0.7021281 object centre at (A) : 19.24800 11.16550 23.38450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8773281E-02 1.4807808E-02 midg,1,midg; midg,igrid,midg 2.1206964E-02 -3.9469108E-02 1,midg,midg; igrid,midg,midg 4.8123486E-02 -1.6013624E-02 gauss-seidel spectral radius is 0.9988524 estimated iterations to convergence 234 setup time was (sec) 0.6400000 now iterating at: 13:11:26 rms-change max change #iterations 4.971033 212.5581 at 10iterations 2.462080 80.59858 at 20iterations 1.223374 34.79272 at 30iterations 0.6135687 17.59190 at 40iterations 0.3067123 9.649271 at 50iterations 0.1530182 4.308154 at 60iterations 7.6497629E-02 2.062714 at 70iterations 3.8429175E-02 1.217822 at 80iterations 1.9349363E-02 0.5672637 at 90iterations 9.7907456E-03 0.2754316 at 100iterations 5.0383322E-03 0.1478119 at 110iterations 2.6786218E-03 8.7490082E-02 at 120iterations finished qdiffx linear iterations at : 13:11:33 total time elapsed so far: 7.700000 # loops : 120 mean,max change (kT/e) : 2.6786218E-03 8.7490082E-02 energy calculations done at 7.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 13:11:33 7.840u 0.210s 0:08.33 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 13:11:33 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 = 2356 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: 3.159576 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): -6.052000 44.54800 ymin,ymax (A): -14.18600 36.51700 zmin,zma (A): 1.247000 45.52200 x,y,z range (A): 50.60000 50.70300 44.27500 scale (grids/A): 3.159576 object centre (A): 19.24800 11.16550 23.38450 number of atom coordinates read : 2356 total number of charged atoms : 2216 net assigned charge : 4.500011 assigned positive charge : 358.3491 centred at (gu) : 87.48397 96.24703 94.30188 assigned negative charge : -353.8496 centred at (gu) : 87.43585 96.85587 94.56725 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 197251 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20915 grid for indexing accessible points = 1.400000 m= 108929 mr = 144092 m= 45260 mr = 90645 m= 13038 mr = 37553 m= 2674 mr = 10139 m= 344 mr = 2050 m= 20 mr = 227 m= 0 mr = 5 time to grow re-entrant surface = 0.6800000 no. cavity mid-points inaccessible to solvent = 1564 time to turn everything in is 1.300000 number of dielectric boundary points 82805 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 17724 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) : 2.106384 object centre at (A) : 19.24800 11.16550 23.38450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4417989 -2.9127689E-02 midg,1,midg; midg,igrid,midg 0.3367100 -0.5295887 1,midg,midg; igrid,midg,midg 0.4687069 -0.5056812 gauss-seidel spectral radius is 0.9993063 estimated iterations to convergence 300 setup time was (sec) 1.530000 now iterating at: 13:11:35 rms-change max change #iterations 11.02820 335.8017 at 10iterations 6.568378 121.9125 at 20iterations 3.912257 75.80871 at 30iterations 2.317832 41.25256 at 40iterations 1.372211 24.03746 at 50iterations 0.8116946 17.65656 at 60iterations 0.4783320 8.129103 at 70iterations 0.2821275 5.214293 at 80iterations 0.1659707 2.747834 at 90iterations 9.7718142E-02 1.601423 at 100iterations 5.7683565E-02 1.075272 at 110iterations 3.4224030E-02 0.5709620 at 120iterations 2.0406237E-02 0.3788910 at 130iterations 1.2436388E-02 0.2126312 at 140iterations 7.7841119E-03 0.1619301 at 150iterations 5.1277010E-03 9.8474503E-02 at 160iterations 3.5883579E-03 7.5302124E-02 at 170iterations 2.6860216E-03 5.6507111E-02 at 180iterations finished qdiffx linear iterations at : 13:11:46 total time elapsed so far: 13.04000 # loops : 180 mean,max change (kT/e) : 2.6860216E-03 5.6507111E-02 energy calculations done at 13.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.18000 DelPhi exited at 13:11:47 13.178u 0.228s 0:13.67 97.9% 0+0k 0+0io 0pf+0w