Tue Oct 11 08:07:19 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 08:07:19 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3037 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5528036 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): 9.515000 72.47100 ymin,ymax (A): -0.9660000 63.43300 zmin,zma (A): -4.963000 41.90500 x,y,z range (A): 62.95600 64.39900 46.86800 scale (grids/A): 0.5528036 object centre (A): 40.99300 31.23350 18.47100 number of atom coordinates read : 3037 total number of charged atoms : 2890 net assigned charge : 8.500035 assigned positive charge : 454.5967 centred at (gu) : 90.34956 90.89469 87.98297 assigned negative charge : -446.0980 centred at (gu) : 90.53928 90.93541 87.87552 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6226 nv = 96 ne = 84 npr = 57498 no. pairs analyzed = 57498 no. exposed pairs = 4245 no. arc points = 31066 no. surface atoms = 1428 nbur = 1609 mkacc time = 0.1700000 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 = 1.540000 m= 276 mr = 2893 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3601 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3146 ## 419 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8005 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.7709330E-10 9.9721942E-10 midg,1,midg; midg,igrid,midg 8.5763741E-10 4.5282320E-10 1,midg,midg; igrid,midg,midg 2.1087201E-09 -1.0262986E-09 gauss-seidel spectral radius is 0.9831460 estimated iterations to convergence 63 setup time was (sec) 0.6500000 now iterating at: 08:07:20 rms-change max change #iterations 7.8152604E-02 13.25101 at 10iterations 5.3677601E-03 0.7927418 at 20iterations 3.6506105E-04 6.6013336E-02 at 30iterations 2.6474374E-05 3.8614273E-03 at 40iterations 2.1129167E-06 2.8800964E-04 at 50iterations finished qdiffx linear iterations at : 08:07:23 total time elapsed so far: 3.930000 # loops : 50 mean,max change (kT/e) : 2.1129167E-06 2.8800964E-04 energy calculations done at 3.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.110000 DelPhi exited at 08:07:23 4.114u 0.243s 0:04.63 93.9% 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 08:07:23 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3037 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.658411 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): 9.515000 72.47100 ymin,ymax (A): -0.9660000 63.43300 zmin,zma (A): -4.963000 41.90500 x,y,z range (A): 62.95600 64.39900 46.86800 scale (grids/A): 1.658411 object centre (A): 40.99300 31.23350 18.47100 number of atom coordinates read : 3037 total number of charged atoms : 2890 net assigned charge : 8.500035 assigned positive charge : 454.5967 centred at (gu) : 91.04755 92.68333 83.94816 assigned negative charge : -446.0980 centred at (gu) : 91.61760 92.80557 83.62626 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 68367 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31066 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 20200 mr = 43353 m= 2085 mr = 13134 m= 54 mr = 910 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 423 time to turn everything in is 0.6200000 number of dielectric boundary points 33308 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 354 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 22140 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) : 0.5528036 object centre at (A) : 40.99300 31.23350 18.47100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.3325712E-03 7.0176166E-03 midg,1,midg; midg,igrid,midg -2.0644823E-03 -1.0223862E-02 1,midg,midg; igrid,midg,midg 2.6804972E-02 -5.9744031E-03 gauss-seidel spectral radius is 0.9982582 estimated iterations to convergence 190 setup time was (sec) 0.9300000 now iterating at: 08:07:25 rms-change max change #iterations 3.450341 189.1488 at 10iterations 1.450886 56.80759 at 20iterations 0.6133014 21.67075 at 30iterations 0.2595182 9.056534 at 40iterations 0.1096148 4.041093 at 50iterations 4.6383392E-02 1.641118 at 60iterations 1.9584298E-02 0.6852508 at 70iterations 8.3331130E-03 0.3152666 at 80iterations 3.5085732E-03 0.1344919 at 90iterations 1.4922685E-03 5.2321553E-02 at 100iterations 6.3213718E-04 2.3101807E-02 at 110iterations 2.6897583E-04 9.5405579E-03 at 120iterations finished qdiffx linear iterations at : 08:07:33 total time elapsed so far: 9.180000 # loops : 120 mean,max change (kT/e) : 2.6897583E-04 9.5405579E-03 energy calculations done at 9.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.350000 DelPhi exited at 08:07:33 9.356u 0.279s 0:09.91 97.0% 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 Tue Oct 11 2011 at 08:07:33 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3037 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.487616 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): 9.515000 72.47100 ymin,ymax (A): -0.9660000 63.43300 zmin,zma (A): -4.963000 41.90500 x,y,z range (A): 62.95600 64.39900 46.86800 scale (grids/A): 2.487616 object centre (A): 40.99300 31.23350 18.47100 number of atom coordinates read : 3037 total number of charged atoms : 2890 net assigned charge : 8.500035 assigned positive charge : 454.5967 centred at (gu) : 91.57104 94.02476 80.92188 assigned negative charge : -446.0980 centred at (gu) : 92.42626 94.20837 80.43925 start vw surface at 0.1800000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 158750 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31066 grid for indexing accessible points = 1.400000 m= 69223 mr = 106872 m= 19549 mr = 52617 m= 3034 mr = 14087 m= 184 mr = 1788 m= 6 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.8700001 no. cavity mid-points inaccessible to solvent = 1396 time to turn everything in is 1.490000 number of dielectric boundary points 75307 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 23096 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) : 1.658411 object centre at (A) : 40.99300 31.23350 18.47100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1760483 8.0153927E-02 midg,1,midg; midg,igrid,midg -4.1279979E-02 -0.1345604 1,midg,midg; igrid,midg,midg 0.3262663 -7.4021383E-03 gauss-seidel spectral radius is 0.9991686 estimated iterations to convergence 274 setup time was (sec) 1.810000 now iterating at: 08:07:35 rms-change max change #iterations 8.988251 308.6750 at 10iterations 5.147219 141.4669 at 20iterations 2.920497 70.42741 at 30iterations 1.647591 35.20715 at 40iterations 0.9252652 19.88488 at 50iterations 0.5190662 11.00142 at 60iterations 0.2898745 6.170435 at 70iterations 0.1618033 3.556868 at 80iterations 9.0101108E-02 1.660502 at 90iterations 5.0186932E-02 0.9578476 at 100iterations 2.7907746E-02 0.5369539 at 110iterations 1.5478800E-02 0.3297706 at 120iterations 8.6281979E-03 0.1741109 at 130iterations 4.7826921E-03 9.8927021E-02 at 140iterations 2.6531131E-03 5.4400206E-02 at 150iterations 1.4696906E-03 3.1412125E-02 at 160iterations 8.1697601E-04 1.6632080E-02 at 170iterations 4.5383361E-04 9.3917847E-03 at 180iterations finished qdiffx linear iterations at : 08:07:49 total time elapsed so far: 15.38000 # loops : 180 mean,max change (kT/e) : 4.5383361E-04 9.3917847E-03 energy calculations done at 15.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.56000 DelPhi exited at 08:07:50 15.566u 0.303s 0:16.38 96.8% 0+0k 0+0io 0pf+0w