Tue Oct 11 03:14:51 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 Tue Oct 11 2011 at 03:14:51 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4361 !!! WARNING: HIR 54 has a net charge of 0.5140 !!! WARNING: HIQ 352 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5197991 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): -9.672000 48.10400 ymin,ymax (A): 29.57200 88.18100 zmin,zma (A): 15.32000 83.80800 x,y,z range (A): 57.77600 58.60900 68.48800 scale (grids/A): 0.5197991 object centre (A): 19.21600 58.87650 49.56400 number of atom coordinates read : 4361 total number of charged atoms : 4210 net assigned charge : 2.8013825E-02 assigned positive charge : 670.6558 centred at (gu) : 90.31372 90.91988 91.16128 assigned negative charge : -670.6318 centred at (gu) : 90.27581 90.86806 91.15527 start vw surface at 0.2000000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 7299 nv = 96 ne = 84 npr = 90137 no. pairs analyzed = 90137 no. exposed pairs = 5172 no. arc points = 35435 no. surface atoms = 1736 nbur = 2625 mkacc time = 0.3000000 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 = 1.652000 m= 248 mr = 3934 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 3600 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3414 ## 451 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 9775 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7417411E-11 2.6397655E-11 midg,1,midg; midg,igrid,midg -1.4830927E-10 2.3222160E-10 1,midg,midg; igrid,midg,midg -1.2742585E-10 1.4432437E-10 gauss-seidel spectral radius is 0.9810315 estimated iterations to convergence 60 setup time was (sec) 0.9200000 now iterating at: 03:14:52 rms-change max change #iterations 7.4843995E-02 13.70009 at 10iterations 4.7173090E-03 0.7320786 at 20iterations 5.8642332E-04 7.7995300E-02 at 30iterations 1.6424607E-04 2.2066116E-02 at 40iterations 5.0151826E-05 6.7691803E-03 at 50iterations finished qdiffx linear iterations at : 03:14:56 total time elapsed so far: 4.560000 # loops : 50 mean,max change (kT/e) : 5.0151826E-05 6.7691803E-03 energy calculations done at 4.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.770000 DelPhi exited at 03:14:56 4.773u 0.409s 0:05.59 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 Tue Oct 11 2011 at 03:14:56 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4361 !!! WARNING: HIR 54 has a net charge of 0.5140 !!! WARNING: HIQ 352 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.559397 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): -9.672000 48.10400 ymin,ymax (A): 29.57200 88.18100 zmin,zma (A): 15.32000 83.80800 x,y,z range (A): 57.77600 58.60900 68.48800 scale (grids/A): 1.559397 object centre (A): 19.21600 58.87650 49.56400 number of atom coordinates read : 4361 total number of charged atoms : 4210 net assigned charge : 2.8013825E-02 assigned positive charge : 670.6558 centred at (gu) : 90.93943 92.75835 93.48203 assigned negative charge : -670.6318 centred at (gu) : 90.82681 92.60369 93.46531 start vw surface at 0.2100000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 81851 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35435 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 24241 mr = 57114 m= 2343 mr = 16897 m= 31 mr = 1105 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 1781 time to turn everything in is 0.8400000 number of dielectric boundary points 33351 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 386 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 31803 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) : 0.5197991 object centre at (A) : 19.21600 58.87650 49.56400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5641819E-03 -2.7183907E-03 midg,1,midg; midg,igrid,midg 5.1716180E-03 1.3029112E-02 1,midg,midg; igrid,midg,midg -1.9702155E-03 -3.2865168E-03 gauss-seidel spectral radius is 0.9981359 estimated iterations to convergence 184 setup time was (sec) 1.170000 now iterating at: 03:14:58 rms-change max change #iterations 3.848512 198.5410 at 10iterations 1.577450 55.03193 at 20iterations 0.6519841 20.67031 at 30iterations 0.2686594 9.077354 at 40iterations 0.1112199 3.536624 at 50iterations 4.5786556E-02 1.513649 at 60iterations 1.9059116E-02 0.6359539 at 70iterations 7.8933658E-03 0.2746124 at 80iterations 3.3079137E-03 0.1199074 at 90iterations 1.4002250E-03 4.7111511E-02 at 100iterations 6.1368803E-04 2.0118713E-02 at 110iterations 2.8273475E-04 9.8066330E-03 at 120iterations finished qdiffx linear iterations at : 03:15:07 total time elapsed so far: 10.40000 # loops : 120 mean,max change (kT/e) : 2.8273475E-04 9.8066330E-03 energy calculations done at 10.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.61000 DelPhi exited at 03:15:08 10.610u 0.464s 0:11.39 97.1% 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 03:15:08 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4361 !!! WARNING: HIR 54 has a net charge of 0.5140 !!! WARNING: HIQ 352 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.339096 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): -9.672000 48.10400 ymin,ymax (A): 29.57200 88.18100 zmin,zma (A): 15.32000 83.80800 x,y,z range (A): 57.77600 58.60900 68.48800 scale (grids/A): 2.339096 object centre (A): 19.21600 58.87650 49.56400 number of atom coordinates read : 4361 total number of charged atoms : 4210 net assigned charge : 2.8013825E-02 assigned positive charge : 670.6558 centred at (gu) : 91.40881 94.13713 95.22257 assigned negative charge : -670.6318 centred at (gu) : 91.24020 93.90549 95.19788 start vw surface at 0.2100000 fill in re-entrant regions at 0.7000000 boundary points on vw surface= 191255 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35435 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 85640 mr = 140234 m= 23279 mr = 68315 m= 3582 mr = 17714 m= 180 mr = 2268 m= 2 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 1.260000 no. cavity mid-points inaccessible to solvent = 6128 time to turn everything in is 2.110000 number of dielectric boundary points 75357 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 42 iepsmp to db, and charging done at 2.280000 number of grid points assigned charge 33608 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) : 1.559397 object centre at (A) : 19.21600 58.87650 49.56400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8453172E-02 2.0994324E-02 midg,1,midg; midg,igrid,midg 0.1241007 0.1996343 1,midg,midg; igrid,midg,midg -7.2483583E-03 -8.0108888E-02 gauss-seidel spectral radius is 0.9991543 estimated iterations to convergence 272 setup time was (sec) 2.490000 now iterating at: 03:15:11 rms-change max change #iterations 10.06922 256.6556 at 10iterations 5.694232 134.1671 at 20iterations 3.204971 87.54821 at 30iterations 1.798298 36.94206 at 40iterations 1.005061 21.37235 at 50iterations 0.5599487 12.93657 at 60iterations 0.3113055 5.781120 at 70iterations 0.1734077 3.505905 at 80iterations 9.6357286E-02 2.801174 at 90iterations 5.3402975E-02 1.017508 at 100iterations 2.9712219E-02 0.6093369 at 110iterations 1.6505143E-02 0.3427200 at 120iterations 9.1670109E-03 0.2024384 at 130iterations 5.0867191E-03 0.1014452 at 140iterations 2.8391180E-03 5.8376312E-02 at 150iterations 1.5922328E-03 3.2754898E-02 at 160iterations 8.9951436E-04 1.6635895E-02 at 170iterations 5.1414088E-04 1.0311127E-02 at 180iterations finished qdiffx linear iterations at : 03:15:26 total time elapsed so far: 17.96000 # loops : 180 mean,max change (kT/e) : 5.1414088E-04 1.0311127E-02 energy calculations done at 17.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.18000 DelPhi exited at 03:15:27 18.186u 0.458s 0:18.96 98.2% 0+0k 0+0io 0pf+0w