Mon Oct 10 17:09:22 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 Mon Oct 10 2011 at 17:09:23 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2894 !!! WARNING: GLY 31 has a net charge of 0.5000 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: ALA 172 has a net charge of 0.5000 !!! WARNING: PRO 352 has a net charge of 0.5000 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: 0.5438934 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): -34.40800 31.04600 ymin,ymax (A): -22.57000 25.10500 zmin,zma (A): -37.95900 6.852000 x,y,z range (A): 65.45400 47.67500 44.81100 scale (grids/A): 0.5438934 object centre (A): -1.681001 1.267500 -15.55350 number of atom coordinates read : 2894 total number of charged atoms : 2754 net assigned charge : 0.5140164 assigned positive charge : 434.3741 centred at (gu) : 89.73919 90.31873 90.21740 assigned negative charge : -433.8612 centred at (gu) : 89.73444 90.16324 90.31400 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5528 nv = 96 ne = 84 npr = 58139 no. pairs analyzed = 58139 no. exposed pairs = 3830 no. arc points = 26861 no. surface atoms = 1293 nbur = 1601 mkacc time = 0.1000000 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 = 1.596000 m= 229 mr = 2735 m= 0 mr = 10 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3012 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2704 ## 336 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7266 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.6945088E-10 -5.8986688E-10 midg,1,midg; midg,igrid,midg -8.5157270E-10 1.0229566E-09 1,midg,midg; igrid,midg,midg 1.0822817E-13 5.3673607E-11 gauss-seidel spectral radius is 0.9825704 estimated iterations to convergence 62 setup time was (sec) 0.4100000 now iterating at: 17:09:23 rms-change max change #iterations 6.9023363E-02 14.68705 at 10iterations 4.6425979E-03 0.7711668 at 20iterations 3.4296306E-04 6.6585541E-02 at 30iterations 4.4332413E-05 1.1456966E-02 at 40iterations 1.0591519E-05 3.0016899E-03 at 50iterations finished qdiffx linear iterations at : 17:09:26 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.0591519E-05 3.0016899E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 17:09:26 3.369u 0.152s 0:03.97 88.4% 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 17:09:27 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2894 !!! WARNING: GLY 31 has a net charge of 0.5000 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: ALA 172 has a net charge of 0.5000 !!! WARNING: PRO 352 has a net charge of 0.5000 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: 1.631680 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): -34.40800 31.04600 ymin,ymax (A): -22.57000 25.10500 zmin,zma (A): -37.95900 6.852000 x,y,z range (A): 65.45400 47.67500 44.81100 scale (grids/A): 1.631680 object centre (A): -1.681001 1.267500 -15.55350 number of atom coordinates read : 2894 total number of charged atoms : 2754 net assigned charge : 0.5140164 assigned positive charge : 434.3741 centred at (gu) : 89.21681 90.95535 90.65124 assigned negative charge : -433.8612 centred at (gu) : 89.20316 90.48930 90.94150 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 60811 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26861 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18563 mr = 39757 m= 1920 mr = 12754 m= 44 mr = 909 m= 0 mr = 2 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 89 time to turn everything in is 0.3000000 number of dielectric boundary points 27916 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 294 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 21052 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) : 0.5438934 object centre at (A) : -1.681001 1.267500 -15.55350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9671546E-03 -2.9338344E-03 midg,1,midg; midg,igrid,midg -1.4338759E-02 1.0715395E-02 1,midg,midg; igrid,midg,midg 2.1091211E-03 -5.0944188E-03 gauss-seidel spectral radius is 0.9981744 estimated iterations to convergence 186 setup time was (sec) 0.5200000 now iterating at: 17:09:27 rms-change max change #iterations 3.293615 180.7344 at 10iterations 1.361551 63.42459 at 20iterations 0.5682024 22.36925 at 30iterations 0.2365326 9.472869 at 40iterations 9.7993173E-02 3.529975 at 50iterations 4.0798258E-02 1.506967 at 60iterations 1.7019570E-02 0.6346111 at 70iterations 7.0979977E-03 0.2679024 at 80iterations 2.9597213E-03 9.8470688E-02 at 90iterations 1.2306173E-03 4.5175552E-02 at 100iterations 5.1660731E-04 1.9122541E-02 at 110iterations 2.1823005E-04 8.1520081E-03 at 120iterations finished qdiffx linear iterations at : 17:09:34 total time elapsed so far: 7.390000 # loops : 120 mean,max change (kT/e) : 2.1823005E-04 8.1520081E-03 energy calculations done at 7.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.530000 DelPhi exited at 17:09:35 7.536u 0.178s 0:08.02 96.0% 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 17:09:35 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2894 !!! WARNING: GLY 31 has a net charge of 0.5000 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: ALA 172 has a net charge of 0.5000 !!! WARNING: PRO 352 has a net charge of 0.5000 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: 2.447520 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): -34.40800 31.04600 ymin,ymax (A): -22.57000 25.10500 zmin,zma (A): -37.95900 6.852000 x,y,z range (A): 65.45400 47.67500 44.81100 scale (grids/A): 2.447520 object centre (A): -1.681001 1.267500 -15.55350 number of atom coordinates read : 2894 total number of charged atoms : 2754 net assigned charge : 0.5140164 assigned positive charge : 434.3741 centred at (gu) : 88.82501 91.43270 90.97667 assigned negative charge : -433.8612 centred at (gu) : 88.80463 90.73378 91.41216 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 141242 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26861 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 63915 mr = 97985 m= 18343 mr = 50034 m= 2849 mr = 13776 m= 186 mr = 1884 m= 3 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 274 time to turn everything in is 0.7300000 number of dielectric boundary points 62774 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 22013 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) : 1.631680 object centre at (A) : -1.681001 1.267500 -15.55350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3939438E-02 -3.6697097E-02 midg,1,midg; midg,igrid,midg -0.2084376 0.1763216 1,midg,midg; igrid,midg,midg 6.8456560E-02 8.4831469E-02 gauss-seidel spectral radius is 0.9991367 estimated iterations to convergence 269 setup time was (sec) 0.9500000 now iterating at: 17:09:36 rms-change max change #iterations 8.591664 301.1696 at 10iterations 4.814280 148.3802 at 20iterations 2.685160 64.09720 at 30iterations 1.492198 37.03566 at 40iterations 0.8231427 19.67295 at 50iterations 0.4546011 10.29393 at 60iterations 0.2503699 5.325377 at 70iterations 0.1380733 3.117476 at 80iterations 7.5873345E-02 1.665577 at 90iterations 4.1698672E-02 0.8671606 at 100iterations 2.2881428E-02 0.4468193 at 110iterations 1.2559461E-02 0.2843895 at 120iterations 6.9007231E-03 0.1510124 at 130iterations 3.7910810E-03 8.4044456E-02 at 140iterations 2.0777676E-03 4.3693542E-02 at 150iterations 1.1428655E-03 2.6944160E-02 at 160iterations 6.2521070E-04 1.2390137E-02 at 170iterations 3.4370567E-04 7.0111752E-03 at 180iterations finished qdiffx linear iterations at : 17:09:47 total time elapsed so far: 11.78000 # loops : 180 mean,max change (kT/e) : 3.4370567E-04 7.0111752E-03 energy calculations done at 11.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.91000 DelPhi exited at 17:09:47 11.908u 0.209s 0:12.44 97.2% 0+0k 0+0io 0pf+0w