Tue Nov 22 14:12:06 PST 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 Tue Nov 22 2011 at 14:12:09 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1948 !!! WARNING: GLM 8 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6021243 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): 8.747001 48.85600 ymin,ymax (A): -15.38300 26.33400 zmin,zma (A): -11.34300 47.78100 x,y,z range (A): 40.10900 41.71700 59.12400 scale (grids/A): 0.6021243 object centre (A): 28.80150 5.475500 18.21900 number of atom coordinates read : 1948 total number of charged atoms : 1812 net assigned charge : 2.906003 assigned positive charge : 287.4381 centred at (gu) : 91.13557 90.28037 89.85920 assigned negative charge : -284.5323 centred at (gu) : 91.23975 90.37861 89.85914 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4628 nv = 96 ne = 84 npr = 40898 no. pairs analyzed = 40898 no. exposed pairs = 2411 no. arc points = 16934 no. surface atoms = 830 nbur = 1118 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 202 mr = 2436 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2369 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1720 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 5711 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4238567E-09 1.3420407E-09 midg,1,midg; midg,igrid,midg 3.8980112E-09 -1.5541191E-09 1,midg,midg; igrid,midg,midg 3.3443615E-09 -2.1405668E-09 gauss-seidel spectral radius is 0.9856665 estimated iterations to convergence 68 setup time was (sec) 0.3800000 now iterating at: 14:12:12 rms-change max change #iterations 9.7328983E-02 16.53114 at 10iterations 8.4797014E-03 1.715141 at 20iterations 6.9387053E-04 0.1355820 at 30iterations 6.0715563E-05 1.1062622E-02 at 40iterations 5.1108809E-06 1.0154247E-03 at 50iterations finished qdiffx linear iterations at : 14:12:23 total time elapsed so far: 3.630000 # loops : 50 mean,max change (kT/e) : 5.1108809E-06 1.0154247E-03 energy calculations done at 3.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.760000 DelPhi exited at 14:12:25 3.760u 0.219s 0:16.39 24.2% 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 Nov 22 2011 at 14:12:27 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1948 !!! WARNING: GLM 8 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.806373 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): 8.747001 48.85600 ymin,ymax (A): -15.38300 26.33400 zmin,zma (A): -11.34300 47.78100 x,y,z range (A): 40.10900 41.71700 59.12400 scale (grids/A): 1.806373 object centre (A): 28.80150 5.475500 18.21900 number of atom coordinates read : 1948 total number of charged atoms : 1812 net assigned charge : 2.906003 assigned positive charge : 287.4381 centred at (gu) : 93.40672 90.84112 89.57763 assigned negative charge : -284.5323 centred at (gu) : 93.71935 91.13601 89.57745 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 49745 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16934 grid for indexing accessible points = 1.400000 m= 16804 mr = 33494 m= 2236 mr = 12216 m= 93 mr = 1319 m= 0 mr = 35 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 95 time to turn everything in is 0.2600000 number of dielectric boundary points 21814 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 156 iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 14157 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) : 0.6021243 object centre at (A) : 28.80150 5.475500 18.21900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9204195E-02 2.4896184E-02 midg,1,midg; midg,igrid,midg 7.9483334E-03 1.2683200E-04 1,midg,midg; igrid,midg,midg 4.9909884E-03 -2.0680632E-03 gauss-seidel spectral radius is 0.9984006 estimated iterations to convergence 198 setup time was (sec) 0.5200000 now iterating at: 14:12:32 rms-change max change #iterations 3.226836 136.3826 at 10iterations 1.417394 59.60912 at 20iterations 0.6240935 24.99473 at 30iterations 0.2744770 11.46621 at 40iterations 0.1212260 4.681669 at 50iterations 5.3108197E-02 1.924567 at 60iterations 2.3356758E-02 0.8893299 at 70iterations 1.0243406E-02 0.3499241 at 80iterations 4.5113382E-03 0.1677437 at 90iterations 1.9789329E-03 7.8479767E-02 at 100iterations 8.6744333E-04 3.2438874E-02 at 110iterations 3.8292643E-04 1.6551971E-02 at 120iterations finished qdiffx linear iterations at : 14:12:58 total time elapsed so far: 8.790000 # loops : 120 mean,max change (kT/e) : 3.8292643E-04 1.6551971E-02 energy calculations done at 8.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.930000 DelPhi exited at 14:12:59 8.935u 0.258s 0:31.77 28.8% 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 Nov 22 2011 at 14:13:00 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1948 !!! WARNING: GLM 8 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.709559 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): 8.747001 48.85600 ymin,ymax (A): -15.38300 26.33400 zmin,zma (A): -11.34300 47.78100 x,y,z range (A): 40.10900 41.71700 59.12400 scale (grids/A): 2.709559 object centre (A): 28.80150 5.475500 18.21900 number of atom coordinates read : 1948 total number of charged atoms : 1812 net assigned charge : 2.906003 assigned positive charge : 287.4381 centred at (gu) : 95.11002 91.26167 89.36642 assigned negative charge : -284.5323 centred at (gu) : 95.57913 91.70403 89.36629 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 114985 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16934 grid for indexing accessible points = 1.400000 m= 55549 mr = 81107 m= 18606 mr = 45160 m= 3728 mr = 14850 m= 437 mr = 2709 m= 18 mr = 287 m= 0 mr = 4 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 342 time to turn everything in is 0.6700000 number of dielectric boundary points 49206 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 14490 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) : 1.806373 object centre at (A) : 28.80150 5.475500 18.21900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2656027 0.2384276 midg,1,midg; midg,igrid,midg 6.1010588E-02 3.4677669E-02 1,midg,midg; igrid,midg,midg 3.2435223E-02 6.7762039E-03 gauss-seidel spectral radius is 0.9991738 estimated iterations to convergence 275 setup time was (sec) 0.9200000 now iterating at: 14:13:03 rms-change max change #iterations 7.799392 370.3516 at 10iterations 4.397022 119.9460 at 20iterations 2.461371 61.20048 at 30iterations 1.372062 35.43948 at 40iterations 0.7647485 18.06322 at 50iterations 0.4254477 9.181242 at 60iterations 0.2361705 5.230621 at 70iterations 0.1313395 2.799207 at 80iterations 7.3036522E-02 1.621750 at 90iterations 4.0493920E-02 0.9313622 at 100iterations 2.2472447E-02 0.4899225 at 110iterations 1.2483775E-02 0.2478096 at 120iterations 6.9450177E-03 0.1448517 at 130iterations 3.8552489E-03 8.0509186E-02 at 140iterations 2.1440226E-03 4.5883179E-02 at 150iterations 1.1894661E-03 2.7425766E-02 at 160iterations 6.5919786E-04 1.3873100E-02 at 170iterations 3.6741587E-04 7.8735352E-03 at 180iterations finished qdiffx linear iterations at : 14:13:29 total time elapsed so far: 13.24000 # loops : 180 mean,max change (kT/e) : 3.6741587E-04 7.8735352E-03 energy calculations done at 13.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.36000 DelPhi exited at 14:13:33 13.365u 0.271s 0:33.22 41.0% 0+0k 0+0io 0pf+0w