Sat Oct 8 16:57:19 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+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 Sat Oct 8 2011 at 16:57:19 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: 364 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4419 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5568852 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): 16.81700 79.06700 ymin,ymax (A): 119.9600 183.8870 zmin,zma (A): -1.298000 59.79000 x,y,z range (A): 62.25000 63.92699 61.08800 scale (grids/A): 0.5568852 object centre (A): 47.94200 151.9235 29.24600 number of atom coordinates read : 4419 total number of charged atoms : 4240 net assigned charge : 2.406049 assigned positive charge : 678.2372 centred at (gu) : 91.66805 89.27666 87.25512 assigned negative charge : -675.8342 centred at (gu) : 91.63302 89.18213 87.24777 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8895 nv = 96 ne = 84 npr = 88487 no. pairs analyzed = 88487 no. exposed pairs = 5352 no. arc points = 37296 no. surface atoms = 1785 nbur = 2634 mkacc time = 0.1900000 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= 382 mr = 4833 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 77 time to turn everything in is 0.4500000 number of dielectric boundary points 4417 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3709 ## 410 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 11560 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2662219E-10 1.7774092E-10 midg,1,midg; midg,igrid,midg -1.4277760E-09 1.3563529E-09 1,midg,midg; igrid,midg,midg -1.9150714E-10 1.1285574E-09 gauss-seidel spectral radius is 0.9834785 estimated iterations to convergence 64 setup time was (sec) 0.6900000 now iterating at: 16:57:20 rms-change max change #iterations 0.1003701 15.67444 at 10iterations 7.4147256E-03 0.9829559 at 20iterations 7.8025059E-04 0.1030397 at 30iterations 1.7972004E-04 2.5718689E-02 at 40iterations 5.1703581E-05 7.2336197E-03 at 50iterations finished qdiffx linear iterations at : 16:57:22 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 5.1703581E-05 7.2336197E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 16:57:23 3.492u 0.226s 0:04.07 91.1% 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 Sat Oct 8 2011 at 16:57:23 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: 364 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4419 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.670656 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): 16.81700 79.06700 ymin,ymax (A): 119.9600 183.8870 zmin,zma (A): -1.298000 59.79000 x,y,z range (A): 62.25000 63.92699 61.08800 scale (grids/A): 1.670656 object centre (A): 47.94200 151.9235 29.24600 number of atom coordinates read : 4419 total number of charged atoms : 4240 net assigned charge : 2.406049 assigned positive charge : 678.2372 centred at (gu) : 95.00320 87.82838 81.76453 assigned negative charge : -675.8342 centred at (gu) : 94.89919 87.54645 81.74332 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 99271 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37296 grid for indexing accessible points = 1.400000 m= 31897 mr = 69542 m= 3978 mr = 22367 m= 146 mr = 2352 m= 0 mr = 36 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 2425 time to turn everything in is 0.7100000 number of dielectric boundary points 40995 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 362 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 32597 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) : 0.5568852 object centre at (A) : 47.94200 151.9235 29.24600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9935703E-03 1.1401992E-02 midg,1,midg; midg,igrid,midg 2.7694596E-02 3.2364376E-02 1,midg,midg; igrid,midg,midg -1.3132838E-02 -2.0836687E-02 gauss-seidel spectral radius is 0.9984061 estimated iterations to convergence 199 setup time was (sec) 1.010000 now iterating at: 16:57:24 rms-change max change #iterations 4.468302 218.2366 at 10iterations 1.953560 89.91900 at 20iterations 0.8623241 28.06700 at 30iterations 0.3803594 13.93510 at 40iterations 0.1678601 6.256306 at 50iterations 7.3850736E-02 2.605682 at 60iterations 3.2630794E-02 0.9201221 at 70iterations 1.4404961E-02 0.4421825 at 80iterations 6.3609621E-03 0.1962032 at 90iterations 2.8353697E-03 8.1981659E-02 at 100iterations 1.2717838E-03 3.7384033E-02 at 110iterations 5.7981577E-04 1.8676758E-02 at 120iterations finished qdiffx linear iterations at : 16:57:31 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 5.7981577E-04 1.8676758E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 16:57:31 7.723u 0.248s 0:08.24 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 Sat Oct 8 2011 at 16:57:31 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: 364 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4419 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.505984 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): 16.81700 79.06700 ymin,ymax (A): 119.9600 183.8870 zmin,zma (A): -1.298000 59.79000 x,y,z range (A): 62.25000 63.92699 61.08800 scale (grids/A): 2.505984 object centre (A): 47.94200 151.9235 29.24600 number of atom coordinates read : 4419 total number of charged atoms : 4240 net assigned charge : 2.406049 assigned positive charge : 678.2372 centred at (gu) : 97.50454 86.74225 77.64674 assigned negative charge : -675.8342 centred at (gu) : 97.34874 86.31959 77.61491 start vw surface at 0.1800000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 230887 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37296 grid for indexing accessible points = 1.400000 m= 109208 mr = 169853 m= 33170 mr = 87427 m= 6688 mr = 25568 m= 632 mr = 4933 m= 17 mr = 376 m= 0 mr = 2 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 8011 time to turn everything in is 1.650000 number of dielectric boundary points 92443 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 33887 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) : 1.670656 object centre at (A) : 47.94200 151.9235 29.24600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5769727E-03 0.2349410 midg,1,midg; midg,igrid,midg 0.5068132 0.4678569 1,midg,midg; igrid,midg,midg -0.1970150 -0.3127709 gauss-seidel spectral radius is 0.9992307 estimated iterations to convergence 285 setup time was (sec) 1.980000 now iterating at: 16:57:33 rms-change max change #iterations 11.25141 415.5768 at 10iterations 6.539497 145.5875 at 20iterations 3.774100 74.58240 at 30iterations 2.174997 40.19810 at 40iterations 1.246627 26.04964 at 50iterations 0.7126342 13.40177 at 60iterations 0.4075660 6.984806 at 70iterations 0.2327679 4.103937 at 80iterations 0.1324303 2.470718 at 90iterations 7.5565033E-02 1.304718 at 100iterations 4.3035455E-02 0.7278404 at 110iterations 2.4497252E-02 0.4146595 at 120iterations 1.3936171E-02 0.2429752 at 130iterations 7.9245614E-03 0.1294394 at 140iterations 4.5113391E-03 6.9625854E-02 at 150iterations 2.5707309E-03 4.4725180E-02 at 160iterations 1.4632400E-03 2.7005196E-02 at 170iterations 8.3609467E-04 1.3185501E-02 at 180iterations finished qdiffx linear iterations at : 16:57:45 total time elapsed so far: 14.12000 # loops : 180 mean,max change (kT/e) : 8.3609467E-04 1.3185501E-02 energy calculations done at 14.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.30000 DelPhi exited at 16:57:46 14.302u 0.236s 0:14.82 98.0% 0+0k 0+0io 0pf+0w