Sun Oct 9 15:49:10 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 15:49:10 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5280 !!! WARNING: HIR 656 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5216041 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): 24.24700 85.69000 ymin,ymax (A): 13.80500 82.05600 zmin,zma (A): -33.32900 31.22100 x,y,z range (A): 61.44300 68.25100 64.55000 scale (grids/A): 0.5216041 object centre (A): 54.96850 47.93050 -1.054001 number of atom coordinates read : 5280 total number of charged atoms : 5110 net assigned charge : -4.485960 assigned positive charge : 806.4998 centred at (gu) : 90.43852 89.70010 90.54627 assigned negative charge : -810.9921 centred at (gu) : 90.32355 89.70252 90.62522 start vw surface at 0.2500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 8884 nv = 96 ne = 84 npr = 108740 no. pairs analyzed = 108740 no. exposed pairs = 6175 no. arc points = 42392 no. surface atoms = 2088 nbur = 3192 mkacc time = 0.2600000 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 = 1.624000 m= 322 mr = 4877 m= 2 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 48 time to turn everything in is 0.5500000 number of dielectric boundary points 4321 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4062 ## 545 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 11834 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2643473E-10 -5.4849009E-10 midg,1,midg; midg,igrid,midg -9.8894545E-11 -1.0604694E-10 1,midg,midg; igrid,midg,midg -5.7831767E-10 4.7855381E-10 gauss-seidel spectral radius is 0.9812232 estimated iterations to convergence 60 setup time was (sec) 0.7700000 now iterating at: 15:49:11 rms-change max change #iterations 8.2255326E-02 10.32475 at 10iterations 8.4314235E-03 1.506744 at 20iterations 2.9848586E-03 0.5477829 at 30iterations 1.2799955E-03 0.2366600 at 40iterations 5.5186613E-04 0.1023979 at 50iterations finished qdiffx linear iterations at : 15:49:14 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 5.5186613E-04 0.1023979 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 15:49:14 3.608u 0.150s 0:04.06 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 15:49:15 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5280 !!! WARNING: HIR 656 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.564812 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): 24.24700 85.69000 ymin,ymax (A): 13.80500 82.05600 zmin,zma (A): -33.32900 31.22100 x,y,z range (A): 61.44300 68.25100 64.55000 scale (grids/A): 1.564812 object centre (A): 54.96850 47.93050 -1.054001 number of atom coordinates read : 5280 total number of charged atoms : 5110 net assigned charge : -4.485960 assigned positive charge : 806.4998 centred at (gu) : 91.31362 89.09891 91.63700 assigned negative charge : -810.9921 centred at (gu) : 90.96999 89.10712 91.87572 start vw surface at 0.2200000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 99835 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42392 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 31084 mr = 70611 m= 3013 mr = 21797 m= 73 mr = 1402 m= 3 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 1786 time to turn everything in is 0.7400000 number of dielectric boundary points 40193 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 493 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 38635 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) : 0.5216041 object centre at (A) : 54.96850 47.93050 -1.054001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3317858E-03 -1.6380737E-02 midg,1,midg; midg,igrid,midg 6.0627232E-03 -1.5162084E-02 1,midg,midg; igrid,midg,midg -9.9798469E-03 1.9327741E-02 gauss-seidel spectral radius is 0.9982278 estimated iterations to convergence 189 setup time was (sec) 1.020000 now iterating at: 15:49:16 rms-change max change #iterations 4.278411 156.6789 at 10iterations 1.800831 57.71501 at 20iterations 0.7603299 24.33895 at 30iterations 0.3212692 10.01303 at 40iterations 0.1365625 4.083843 at 50iterations 5.8221985E-02 1.806781 at 60iterations 2.5507534E-02 0.7671242 at 70iterations 1.1782479E-02 0.3713913 at 80iterations 6.0557015E-03 0.2243614 at 90iterations 3.6395635E-03 0.1341171 at 100iterations 2.4329263E-03 8.6124420E-02 at 110iterations 1.7301468E-03 6.2896729E-02 at 120iterations finished qdiffx linear iterations at : 15:49:22 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 1.7301468E-03 6.2896729E-02 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 15:49:23 7.761u 0.180s 0:08.24 96.3% 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 15:49:23 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5280 !!! WARNING: HIR 656 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.347218 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): 24.24700 85.69000 ymin,ymax (A): 13.80500 82.05600 zmin,zma (A): -33.32900 31.22100 x,y,z range (A): 61.44300 68.25100 64.55000 scale (grids/A): 2.347218 object centre (A): 54.96850 47.93050 -1.054001 number of atom coordinates read : 5280 total number of charged atoms : 5110 net assigned charge : -4.485960 assigned positive charge : 806.4998 centred at (gu) : 91.96977 88.64815 92.45490 assigned negative charge : -810.9921 centred at (gu) : 91.45522 88.66057 92.81377 start vw surface at 0.2300000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 232571 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42392 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 108739 mr = 172671 m= 30374 mr = 87338 m= 4510 mr = 22861 m= 251 mr = 2889 m= 3 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 5778 time to turn everything in is 1.770000 number of dielectric boundary points 90608 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 43 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 40811 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) : 1.564812 object centre at (A) : 54.96850 47.93050 -1.054001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.4215244E-02 -0.1905652 midg,1,midg; midg,igrid,midg 0.1433093 -0.2697762 1,midg,midg; igrid,midg,midg -0.1211545 0.4037075 gauss-seidel spectral radius is 0.9991982 estimated iterations to convergence 279 setup time was (sec) 2.080000 now iterating at: 15:49:25 rms-change max change #iterations 11.28452 279.0866 at 10iterations 6.507327 144.9163 at 20iterations 3.721156 74.12796 at 30iterations 2.122190 43.32674 at 40iterations 1.206317 22.60956 at 50iterations 0.6836951 14.07024 at 60iterations 0.3865336 7.387295 at 70iterations 0.2186875 3.752615 at 80iterations 0.1234517 2.393962 at 90iterations 6.9733433E-02 1.295925 at 100iterations 3.9483637E-02 0.6661835 at 110iterations 2.2465993E-02 0.3884830 at 120iterations 1.2898449E-02 0.2640495 at 130iterations 7.5376322E-03 0.1517048 at 140iterations 4.5868480E-03 8.8493347E-02 at 150iterations 2.9375192E-03 5.9982300E-02 at 160iterations 2.0037557E-03 4.5509338E-02 at 170iterations 1.4665766E-03 3.1803131E-02 at 180iterations finished qdiffx linear iterations at : 15:49:36 total time elapsed so far: 12.58000 # loops : 180 mean,max change (kT/e) : 1.4665766E-03 3.1803131E-02 energy calculations done at 12.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.77000 DelPhi exited at 15:49:36 12.775u 0.178s 0:13.25 97.6% 0+0k 0+0io 0pf+0w