Sat Oct 15 13:13:32 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 15 2011 at 13:13:32 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5678 !!! WARNING: HIR 147 has a net charge of 0.5140 !!! WARNING: HIR 555 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= 0.1600000 grid size : 179 scale,in grids/A, set to be: 0.5000774 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): 67.38900 138.5780 ymin,ymax (A): -6.240000 57.13200 zmin,zma (A): -3.422000 65.99000 x,y,z range (A): 71.18899 63.37200 69.41199 scale (grids/A): 0.5000774 object centre (A): 102.9835 25.44600 31.28400 number of atom coordinates read : 5678 total number of charged atoms : 5507 net assigned charge : -2.471966 assigned positive charge : 870.6932 centred at (gu) : 89.71555 90.84150 90.15607 assigned negative charge : -873.1730 centred at (gu) : 89.77580 90.77673 90.25134 start vw surface at 0.2600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 8520 nv = 96 ne = 84 npr = 118516 no. pairs analyzed = 118516 no. exposed pairs = 6584 no. arc points = 44695 no. surface atoms = 2233 nbur = 3445 mkacc time = 0.3400000 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 = 1.708000 m= 282 mr = 4572 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.6500000 number of dielectric boundary points 4227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4362 ## 661 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 11757 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5863860E-10 -2.2567018E-10 midg,1,midg; midg,igrid,midg -1.2256528E-10 1.3347513E-10 1,midg,midg; igrid,midg,midg 1.0477471E-10 -1.3389198E-10 gauss-seidel spectral radius is 0.9796033 estimated iterations to convergence 58 setup time was (sec) 0.9300000 now iterating at: 13:13:33 rms-change max change #iterations 6.7291714E-02 9.899237 at 10iterations 4.8590261E-03 0.6773605 at 20iterations 1.0187546E-03 0.1861668 at 30iterations 3.0944767E-04 5.5961609E-02 at 40iterations 9.7164921E-05 1.7019272E-02 at 50iterations finished qdiffx linear iterations at : 13:13:36 total time elapsed so far: 4.090000 # loops : 50 mean,max change (kT/e) : 9.7164921E-05 1.7019272E-02 energy calculations done at 4.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.320000 DelPhi exited at 13:13:37 4.323u 0.180s 0:04.87 92.4% 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 Sat Oct 15 2011 at 13:13:37 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5678 !!! WARNING: HIR 147 has a net charge of 0.5140 !!! WARNING: HIR 555 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= 0.1800000 grid size : 179 scale,in grids/A, set to be: 1.500232 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): 67.38900 138.5780 ymin,ymax (A): -6.240000 57.13200 zmin,zma (A): -3.422000 65.99000 x,y,z range (A): 71.18899 63.37200 69.41199 scale (grids/A): 1.500232 object centre (A): 102.9835 25.44600 31.28400 number of atom coordinates read : 5678 total number of charged atoms : 5507 net assigned charge : -2.471966 assigned positive charge : 870.6932 centred at (gu) : 89.14500 92.52282 90.46619 assigned negative charge : -873.1730 centred at (gu) : 89.32740 92.32996 90.75404 start vw surface at 0.2700000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 96800 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44695 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 28781 mr = 67604 m= 2600 mr = 19726 m= 58 mr = 1133 m= 0 mr = 4 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 1589 time to turn everything in is 0.8900000 number of dielectric boundary points 39772 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 606 ## 10 charges are in solution ## iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 41152 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) : 0.5000774 object centre at (A) : 102.9835 25.44600 31.28400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7215495E-03 3.0147454E-03 midg,1,midg; midg,igrid,midg -1.0958474E-02 5.6037842E-03 1,midg,midg; igrid,midg,midg -1.6622778E-02 -7.4694557E-03 gauss-seidel spectral radius is 0.9980864 estimated iterations to convergence 182 setup time was (sec) 1.240000 now iterating at: 13:13:38 rms-change max change #iterations 4.044948 165.0293 at 10iterations 1.647386 58.22101 at 20iterations 0.6710898 21.24290 at 30iterations 0.2742169 9.162680 at 40iterations 0.1117454 3.952564 at 50iterations 4.5876298E-02 1.567570 at 60iterations 1.8786928E-02 0.5540457 at 70iterations 7.7534416E-03 0.2347183 at 80iterations 3.2382826E-03 0.1144867 at 90iterations 1.3945813E-03 4.7026157E-02 at 100iterations 6.3411455E-04 2.1816254E-02 at 110iterations 3.1450711E-04 1.2231827E-02 at 120iterations finished qdiffx linear iterations at : 13:13:46 total time elapsed so far: 9.120000 # loops : 120 mean,max change (kT/e) : 3.1450711E-04 1.2231827E-02 energy calculations done at 9.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.350000 DelPhi exited at 13:13:47 9.350u 0.219s 0:09.89 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 15 2011 at 13:13:47 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5678 !!! WARNING: HIR 147 has a net charge of 0.5140 !!! WARNING: HIR 555 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= 0.1700000 grid size : 179 scale,in grids/A, set to be: 2.250348 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): 67.38900 138.5780 ymin,ymax (A): -6.240000 57.13200 zmin,zma (A): -3.422000 65.99000 x,y,z range (A): 71.18899 63.37200 69.41199 scale (grids/A): 2.250348 object centre (A): 102.9835 25.44600 31.28400 number of atom coordinates read : 5678 total number of charged atoms : 5507 net assigned charge : -2.471966 assigned positive charge : 870.6932 centred at (gu) : 88.71706 93.78371 90.69888 assigned negative charge : -873.1730 centred at (gu) : 88.99102 93.49490 91.13103 start vw surface at 0.2700000 fill in re-entrant regions at 0.7200000 boundary points on vw surface= 226011 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44695 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 102210 mr = 166400 m= 27478 mr = 80589 m= 3751 mr = 20511 m= 165 mr = 2233 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 1.240000 no. cavity mid-points inaccessible to solvent = 5036 time to turn everything in is 2.100000 number of dielectric boundary points 89843 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 112 iepsmp to db, and charging done at 2.290000 number of grid points assigned charge 43923 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) : 1.500232 object centre at (A) : 102.9835 25.44600 31.28400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5921063E-02 0.1807927 midg,1,midg; midg,igrid,midg -0.2436210 0.1842328 1,midg,midg; igrid,midg,midg -0.4963668 0.1652806 gauss-seidel spectral radius is 0.9991649 estimated iterations to convergence 273 setup time was (sec) 2.490000 now iterating at: 13:13:50 rms-change max change #iterations 11.02758 250.9332 at 10iterations 6.278099 143.5547 at 20iterations 3.556739 84.13746 at 30iterations 2.003268 37.70304 at 40iterations 1.126635 27.19402 at 50iterations 0.6316397 12.90846 at 60iterations 0.3532248 7.413778 at 70iterations 0.1971697 3.360931 at 80iterations 0.1100150 2.104222 at 90iterations 6.1196189E-02 1.174397 at 100iterations 3.4206025E-02 0.6129198 at 110iterations 1.9001767E-02 0.3662758 at 120iterations 1.0588311E-02 0.1862907 at 130iterations 5.8926479E-03 0.1169186 at 140iterations 3.2880334E-03 6.0593605E-02 at 150iterations 1.8296093E-03 3.6426544E-02 at 160iterations 1.0251970E-03 1.7528534E-02 at 170iterations 5.7747879E-04 1.0692596E-02 at 180iterations finished qdiffx linear iterations at : 13:14:02 total time elapsed so far: 15.10000 # loops : 180 mean,max change (kT/e) : 5.7747879E-04 1.0692596E-02 energy calculations done at 15.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.33000 DelPhi exited at 13:14:03 15.333u 0.222s 0:15.95 97.4% 0+0k 0+0io 0pf+0w