Mon Oct 10 11:34:29 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 Mon Oct 10 2011 at 11:34:29 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 0.7402324 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): 8.350000 56.44300 ymin,ymax (A): -9.050000 36.47600 zmin,zma (A): -3.021000 44.31500 x,y,z range (A): 48.09300 45.52600 47.33600 scale (grids/A): 0.7402324 object centre (A): 32.39650 13.71300 20.64700 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 89.66545 90.55293 89.80875 assigned negative charge : -323.3720 centred at (gu) : 89.67674 90.63585 90.01470 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8046 nv = 96 ne = 84 npr = 43229 no. pairs analyzed = 43229 no. exposed pairs = 2672 no. arc points = 18948 no. surface atoms = 905 nbur = 1212 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 568 mr = 4506 m= 5 mr = 126 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 66 time to turn everything in is 0.2600000 number of dielectric boundary points 3987 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1527 ## 122 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 8441 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0138598E-07 -3.1589579E-07 midg,1,midg; midg,igrid,midg -2.3994730E-08 -2.1831642E-07 1,midg,midg; igrid,midg,midg -1.0527077E-07 -1.1525662E-07 gauss-seidel spectral radius is 0.9904919 estimated iterations to convergence 83 setup time was (sec) 0.4900000 now iterating at: 11:34:30 rms-change max change #iterations 0.2465384 34.37495 at 10iterations 3.3522144E-02 4.425583 at 20iterations 4.4712778E-03 0.5176773 at 30iterations 6.0427526E-04 7.4996948E-02 at 40iterations 8.2102029E-05 9.2926025E-03 at 50iterations finished qdiffx linear iterations at : 11:34:33 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 8.2102029E-05 9.2926025E-03 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 11:34:33 3.273u 0.231s 0:03.85 90.9% 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 Mon Oct 10 2011 at 11:34:33 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 2.220697 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): 8.350000 56.44300 ymin,ymax (A): -9.050000 36.47600 zmin,zma (A): -3.021000 44.31500 x,y,z range (A): 48.09300 45.52600 47.33600 scale (grids/A): 2.220697 object centre (A): 32.39650 13.71300 20.64700 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 88.99622 91.65868 89.42598 assigned negative charge : -323.3720 centred at (gu) : 89.03026 91.90724 90.04416 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 84753 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18948 grid for indexing accessible points = 1.400000 m= 34132 mr = 58777 m= 7418 mr = 26170 m= 838 mr = 5197 m= 29 mr = 489 m= 0 mr = 1 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1590 time to turn everything in is 0.6100000 number of dielectric boundary points 36536 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 41 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 15752 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) : 0.7402324 object centre at (A) : 32.39650 13.71300 20.64700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.4498776E-03 -0.1250869 midg,1,midg; midg,igrid,midg -2.7331650E-02 -4.4943631E-02 1,midg,midg; igrid,midg,midg 4.4155405E-03 2.0245528E-03 gauss-seidel spectral radius is 0.9989284 estimated iterations to convergence 242 setup time was (sec) 0.9000000 now iterating at: 11:34:34 rms-change max change #iterations 5.120074 232.5268 at 10iterations 2.599820 76.27325 at 20iterations 1.327753 37.12338 at 30iterations 0.6770642 19.31891 at 40iterations 0.3453158 9.330888 at 50iterations 0.1758331 4.589001 at 60iterations 8.9662038E-02 2.626203 at 70iterations 4.5930136E-02 1.396112 at 80iterations 2.3419011E-02 0.6703148 at 90iterations 1.1933364E-02 0.3646507 at 100iterations 6.0880510E-03 0.1803573 at 110iterations 3.1177658E-03 9.2264175E-02 at 120iterations finished qdiffx linear iterations at : 11:34:42 total time elapsed so far: 8.250000 # loops : 120 mean,max change (kT/e) : 3.1177658E-03 9.2264175E-02 energy calculations done at 8.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.410000 DelPhi exited at 11:34:42 8.417u 0.252s 0:08.98 96.4% 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 Mon Oct 10 2011 at 11:34:42 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.331046 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): 8.350000 56.44300 ymin,ymax (A): -9.050000 36.47600 zmin,zma (A): -3.021000 44.31500 x,y,z range (A): 48.09300 45.52600 47.33600 scale (grids/A): 3.331046 object centre (A): 32.39650 13.71300 20.64700 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 88.49423 92.48794 89.13889 assigned negative charge : -323.3720 centred at (gu) : 88.54543 92.86083 90.06628 start vw surface at 0.1300000 fill in re-entrant regions at 0.8800000 boundary points on vw surface= 194920 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18948 grid for indexing accessible points = 1.400000 m= 104222 mr = 141199 m= 45035 mr = 86769 m= 14254 mr = 37581 m= 3343 mr = 11385 m= 501 mr = 2635 m= 26 mr = 327 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 5408 time to turn everything in is 1.960000 number of dielectric boundary points 82396 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.100000 number of grid points assigned charge 15824 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) : 2.220697 object centre at (A) : 32.39650 13.71300 20.64700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1681300 -1.183111 midg,1,midg; midg,igrid,midg -0.2438968 -0.2533606 1,midg,midg; igrid,midg,midg 1.8083991E-02 2.7070925E-02 gauss-seidel spectral radius is 0.9993181 estimated iterations to convergence 302 setup time was (sec) 2.280000 now iterating at: 11:34:45 rms-change max change #iterations 11.00396 387.2010 at 10iterations 6.483580 140.8472 at 20iterations 3.826982 67.72823 at 30iterations 2.245278 44.48119 at 40iterations 1.321371 23.11526 at 50iterations 0.7790381 13.11853 at 60iterations 0.4572307 7.649292 at 70iterations 0.2677054 4.374599 at 80iterations 0.1576150 2.738064 at 90iterations 9.2678033E-02 1.473299 at 100iterations 5.4400735E-02 1.041626 at 110iterations 3.1924423E-02 0.5735793 at 120iterations 1.8741818E-02 0.3198586 at 130iterations 1.1016466E-02 0.1748961 at 140iterations 6.4698299E-03 0.1059246 at 150iterations 3.7961025E-03 6.3199759E-02 at 160iterations 2.2299381E-03 3.6457062E-02 at 170iterations 1.3094177E-03 2.1171570E-02 at 180iterations finished qdiffx linear iterations at : 11:34:55 total time elapsed so far: 12.79000 # loops : 180 mean,max change (kT/e) : 1.3094177E-03 2.1171570E-02 energy calculations done at 12.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.97000 DelPhi exited at 11:34:56 12.970u 0.239s 0:13.53 97.5% 0+0k 0+0io 0pf+0w