Tue Oct 11 03:16:32 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+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 Tue Oct 11 2011 at 03:16:33 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5166 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: 0.5083826 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): 10.34200 80.36800 ymin,ymax (A): -0.1940000 66.22000 zmin,zma (A): 6.705000 69.12600 x,y,z range (A): 70.02600 66.41400 62.42100 scale (grids/A): 0.5083826 object centre (A): 45.35500 33.01300 37.91550 number of atom coordinates read : 5166 total number of charged atoms : 5068 net assigned charge : 2.500010 assigned positive charge : 805.6765 centred at (gu) : 90.78604 89.96165 90.26858 assigned negative charge : -803.1832 centred at (gu) : 90.78873 89.89864 90.26800 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8342 nv = 96 ne = 84 npr = 104191 no. pairs analyzed = 104191 no. exposed pairs = 6310 no. arc points = 43418 no. surface atoms = 2107 nbur = 3059 mkacc time = 0.2200000 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 = 1.680000 m= 308 mr = 4463 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.4800000 number of dielectric boundary points 4183 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4231 ## 615 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 11424 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8649987E-11 3.6191893E-11 midg,1,midg; midg,igrid,midg -1.3776541E-10 1.9594855E-10 1,midg,midg; igrid,midg,midg 3.2128619E-11 3.0671406E-11 gauss-seidel spectral radius is 0.9802368 estimated iterations to convergence 59 setup time was (sec) 0.7300000 now iterating at: 03:16:34 rms-change max change #iterations 7.3561035E-02 11.48840 at 10iterations 4.1527995E-03 0.5662947 at 20iterations 4.4308606E-04 5.5168152E-02 at 30iterations 1.2740052E-04 1.5435219E-02 at 40iterations 4.2174161E-05 5.4073334E-03 at 50iterations finished qdiffx linear iterations at : 03:16:36 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 4.2174161E-05 5.4073334E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 03:16:37 3.508u 0.175s 0:04.21 87.1% 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 Tue Oct 11 2011 at 03:16:37 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5166 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.525148 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): 10.34200 80.36800 ymin,ymax (A): -0.1940000 66.22000 zmin,zma (A): 6.705000 69.12600 x,y,z range (A): 70.02600 66.41400 62.42100 scale (grids/A): 1.525148 object centre (A): 45.35500 33.01300 37.91550 number of atom coordinates read : 5166 total number of charged atoms : 5068 net assigned charge : 2.500010 assigned positive charge : 805.6765 centred at (gu) : 92.35632 89.88281 90.80383 assigned negative charge : -803.1832 centred at (gu) : 92.36550 89.69571 90.80352 start vw surface at 0.2100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 94481 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43418 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 28728 mr = 65832 m= 2316 mr = 19810 m= 32 mr = 946 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 2651 time to turn everything in is 0.6600000 number of dielectric boundary points 38969 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 525 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 38016 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) : 0.5083826 object centre at (A) : 45.35500 33.01300 37.91550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3439504E-02 1.0678604E-02 midg,1,midg; midg,igrid,midg -1.0176338E-02 2.1117560E-03 1,midg,midg; igrid,midg,midg 1.1158083E-03 -5.8084109E-04 gauss-seidel spectral radius is 0.9981321 estimated iterations to convergence 184 setup time was (sec) 0.9500000 now iterating at: 03:16:38 rms-change max change #iterations 4.055600 150.5898 at 10iterations 1.666880 57.95319 at 20iterations 0.6878518 21.52297 at 30iterations 0.2829562 9.108006 at 40iterations 0.1163247 3.537180 at 50iterations 4.8024468E-02 1.498062 at 60iterations 1.9879729E-02 0.6524658 at 70iterations 8.2204388E-03 0.2589970 at 80iterations 3.4091836E-03 0.1090719 at 90iterations 1.4231087E-03 4.6686172E-02 at 100iterations 6.0451176E-04 1.8337250E-02 at 110iterations 2.6607193E-04 8.1138611E-03 at 120iterations finished qdiffx linear iterations at : 03:16:45 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 2.6607193E-04 8.1138611E-03 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 03:16:45 7.855u 0.218s 0:08.49 94.9% 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 Tue Oct 11 2011 at 03:16:45 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5166 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.287722 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): 10.34200 80.36800 ymin,ymax (A): -0.1940000 66.22000 zmin,zma (A): 6.705000 69.12600 x,y,z range (A): 70.02600 66.41400 62.42100 scale (grids/A): 2.287722 object centre (A): 45.35500 33.01300 37.91550 number of atom coordinates read : 5166 total number of charged atoms : 5068 net assigned charge : 2.500010 assigned positive charge : 805.6765 centred at (gu) : 93.53402 89.82373 91.20525 assigned negative charge : -803.1832 centred at (gu) : 93.54824 89.54341 91.20522 start vw surface at 0.2200000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 220164 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43418 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 102188 mr = 161177 m= 26258 mr = 81335 m= 3176 mr = 19306 m= 107 mr = 1801 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 8623 time to turn everything in is 1.570000 number of dielectric boundary points 88260 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 54 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 40441 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) : 1.525148 object centre at (A) : 45.35500 33.01300 37.91550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2364026 0.1691210 midg,1,midg; midg,igrid,midg -0.1218455 1.4266151E-02 1,midg,midg; igrid,midg,midg -3.0092541E-03 -2.8209820E-02 gauss-seidel spectral radius is 0.9991745 estimated iterations to convergence 275 setup time was (sec) 1.890000 now iterating at: 03:16:48 rms-change max change #iterations 10.92878 353.0958 at 10iterations 6.288229 149.5359 at 20iterations 3.592432 72.59778 at 30iterations 2.043798 41.59660 at 40iterations 1.157234 24.00540 at 50iterations 0.6529214 12.69449 at 60iterations 0.3681264 7.141774 at 70iterations 0.2073682 4.117191 at 80iterations 0.1164203 2.243340 at 90iterations 6.5336123E-02 1.226826 at 100iterations 3.6604188E-02 0.7041335 at 110iterations 2.0439772E-02 0.3843203 at 120iterations 1.1473287E-02 0.1993771 at 130iterations 6.4179944E-03 0.1118469 at 140iterations 3.5946327E-03 6.9396973E-02 at 150iterations 2.0115902E-03 3.7120819E-02 at 160iterations 1.1309169E-03 1.9638062E-02 at 170iterations 6.3971168E-04 1.2681961E-02 at 180iterations finished qdiffx linear iterations at : 03:16:59 total time elapsed so far: 13.69000 # loops : 180 mean,max change (kT/e) : 6.3971168E-04 1.2681961E-02 energy calculations done at 13.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.86000 DelPhi exited at 03:17:00 13.860u 0.235s 0:14.50 97.1% 0+0k 0+0io 0pf+0w