Sun Oct 9 23:00:04 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 23:00:04 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 = 3980 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5649000 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): -32.05000 20.05400 ymin,ymax (A): -81.89100 -18.87100 zmin,zma (A): -2.177000 54.43500 x,y,z range (A): 52.10400 63.02000 56.61200 scale (grids/A): 0.5649000 object centre (A): -5.998000 -50.38100 26.12900 number of atom coordinates read : 3980 total number of charged atoms : 3822 net assigned charge : 1.5646219E-05 assigned positive charge : 598.2686 centred at (gu) : 91.35745 89.26968 89.93839 assigned negative charge : -598.2725 centred at (gu) : 91.14716 89.28771 89.99596 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 8411 nv = 96 ne = 84 npr = 79029 no. pairs analyzed = 79029 no. exposed pairs = 5243 no. arc points = 36409 no. surface atoms = 1759 nbur = 2221 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 373 mr = 4392 m= 0 mr = 24 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 4368 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3680 ## 448 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 10929 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.7041253E-10 -1.0656738E-09 midg,1,midg; midg,igrid,midg 3.1423586E-10 -3.1459699E-10 1,midg,midg; igrid,midg,midg -2.7877369E-09 4.9875601E-09 gauss-seidel spectral radius is 0.9839183 estimated iterations to convergence 65 setup time was (sec) 0.4500000 now iterating at: 23:00:04 rms-change max change #iterations 9.9988177E-02 13.23343 at 10iterations 7.5232657E-03 0.9893618 at 20iterations 6.2778563E-04 9.8846436E-02 at 30iterations 1.2224825E-04 2.6906967E-02 at 40iterations 4.6117588E-05 1.0566711E-02 at 50iterations finished qdiffx linear iterations at : 23:00:07 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 4.6117588E-05 1.0566711E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 23:00:08 3.422u 0.169s 0:03.89 92.0% 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 23:00:08 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 = 3980 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.694700 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): -32.05000 20.05400 ymin,ymax (A): -81.89100 -18.87100 zmin,zma (A): -2.177000 54.43500 x,y,z range (A): 52.10400 63.02000 56.61200 scale (grids/A): 1.694700 object centre (A): -5.998000 -50.38100 26.12900 number of atom coordinates read : 3980 total number of charged atoms : 3822 net assigned charge : 1.5646219E-05 assigned positive charge : 598.2686 centred at (gu) : 94.07061 87.80726 89.81358 assigned negative charge : -598.2725 centred at (gu) : 93.44080 87.86286 89.98741 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 93449 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36409 grid for indexing accessible points = 1.400000 m= 29992 mr = 63878 m= 3448 mr = 20832 m= 131 mr = 1809 m= 0 mr = 20 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 95 time to turn everything in is 0.4300000 number of dielectric boundary points 40481 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 389 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 29497 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) : 0.5649000 object centre at (A) : -5.998000 -50.38100 26.12900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.6834619E-03 1.0264389E-03 midg,1,midg; midg,igrid,midg 2.4921505E-02 1.0024902E-02 1,midg,midg; igrid,midg,midg -2.4401493E-02 -8.5792464E-04 gauss-seidel spectral radius is 0.9984314 estimated iterations to convergence 200 setup time was (sec) 0.6300000 now iterating at: 23:00:09 rms-change max change #iterations 4.273974 163.2169 at 10iterations 1.884493 57.12357 at 20iterations 0.8303598 26.60637 at 30iterations 0.3683720 12.73770 at 40iterations 0.1631337 4.804929 at 50iterations 7.2350614E-02 2.171396 at 60iterations 3.2140292E-02 0.9528923 at 70iterations 1.4220186E-02 0.3928680 at 80iterations 6.3206200E-03 0.1990008 at 90iterations 2.8144352E-03 8.0913544E-02 at 100iterations 1.2634934E-03 3.9234161E-02 at 110iterations 5.7087821E-04 1.7723083E-02 at 120iterations finished qdiffx linear iterations at : 23:00:16 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 5.7087821E-04 1.7723083E-02 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 23:00:16 7.804u 0.210s 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 Sun Oct 9 2011 at 23:00:16 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 = 3980 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.542050 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): -32.05000 20.05400 ymin,ymax (A): -81.89100 -18.87100 zmin,zma (A): -2.177000 54.43500 x,y,z range (A): 52.10400 63.02000 56.61200 scale (grids/A): 2.542050 object centre (A): -5.998000 -50.38100 26.12900 number of atom coordinates read : 3980 total number of charged atoms : 3822 net assigned charge : 1.5646219E-05 assigned positive charge : 598.2686 centred at (gu) : 96.10533 86.71046 89.71991 assigned negative charge : -598.2725 centred at (gu) : 95.16093 86.79404 89.98080 start vw surface at 0.1100000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 216971 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36409 grid for indexing accessible points = 1.400000 m= 102616 mr = 156201 m= 30274 mr = 81653 m= 5484 mr = 22803 m= 473 mr = 3780 m= 11 mr = 277 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 296 time to turn everything in is 1.100000 number of dielectric boundary points 91115 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 30551 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) : 1.694700 object centre at (A) : -5.998000 -50.38100 26.12900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1292696 -1.9332839E-02 midg,1,midg; midg,igrid,midg 0.2436042 0.3462870 1,midg,midg; igrid,midg,midg -0.2570141 -4.8061568E-02 gauss-seidel spectral radius is 0.9992420 estimated iterations to convergence 287 setup time was (sec) 1.350000 now iterating at: 23:00:18 rms-change max change #iterations 10.96585 349.4042 at 10iterations 6.510676 151.0671 at 20iterations 3.819839 78.07697 at 30iterations 2.225690 45.00914 at 40iterations 1.293161 26.14188 at 50iterations 0.7498013 14.63737 at 60iterations 0.4332613 8.439428 at 70iterations 0.2492108 4.739037 at 80iterations 0.1432019 2.914367 at 90iterations 8.2091779E-02 1.626453 at 100iterations 4.7216695E-02 0.8216707 at 110iterations 2.7079357E-02 0.4766502 at 120iterations 1.5479566E-02 0.2833061 at 130iterations 8.8576050E-03 0.1596680 at 140iterations 5.0861994E-03 9.9637985E-02 at 150iterations 2.9131151E-03 5.1101685E-02 at 160iterations 1.6707194E-03 2.9584885E-02 at 170iterations 9.6353621E-04 1.5620708E-02 at 180iterations finished qdiffx linear iterations at : 23:00:29 total time elapsed so far: 13.04000 # loops : 180 mean,max change (kT/e) : 9.6353621E-04 1.5620708E-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) 13.17000 DelPhi exited at 23:00:30 13.169u 0.212s 0:13.64 98.0% 0+0k 0+0io 0pf+0w