Tue Oct 11 05:25:51 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 05:25:51 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2189 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7431995 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): 25.70500 72.28900 ymin,ymax (A): -18.91500 28.98600 zmin,zma (A): 3.944000 46.44700 x,y,z range (A): 46.58400 47.90100 42.50300 scale (grids/A): 0.7431995 object centre (A): 48.99700 5.035501 25.19550 number of atom coordinates read : 2189 total number of charged atoms : 1910 net assigned charge : 7.500009 assigned positive charge : 309.4701 centred at (gu) : 88.97322 90.63111 90.22248 assigned negative charge : -301.9702 centred at (gu) : 89.12269 90.51392 90.30042 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7858 nv = 96 ne = 84 npr = 38728 no. pairs analyzed = 38728 no. exposed pairs = 2499 no. arc points = 17075 no. surface atoms = 856 nbur = 1333 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 616 mr = 4617 m= 2 mr = 142 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3717 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1478 ## 122 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8131 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0965939E-07 6.1226608E-08 midg,1,midg; midg,igrid,midg 1.7053413E-08 2.8977865E-07 1,midg,midg; igrid,midg,midg 3.5116435E-07 -1.1458449E-08 gauss-seidel spectral radius is 0.9905518 estimated iterations to convergence 84 setup time was (sec) 0.5400000 now iterating at: 05:25:52 rms-change max change #iterations 0.2455930 32.21034 at 10iterations 3.3299040E-02 4.242691 at 20iterations 4.8461715E-03 0.6177826 at 30iterations 8.2056457E-04 0.1012230 at 40iterations 2.0507726E-04 2.1545410E-02 at 50iterations finished qdiffx linear iterations at : 05:25:55 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 2.0507726E-04 2.1545410E-02 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 05:25:55 3.609u 0.192s 0:04.11 92.2% 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 Oct 11 2011 at 05:25:55 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2189 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.229599 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): 25.70500 72.28900 ymin,ymax (A): -18.91500 28.98600 zmin,zma (A): 3.944000 46.44700 x,y,z range (A): 46.58400 47.90100 42.50300 scale (grids/A): 2.229599 object centre (A): 48.99700 5.035501 25.19550 number of atom coordinates read : 2189 total number of charged atoms : 1910 net assigned charge : 7.500009 assigned positive charge : 309.4701 centred at (gu) : 86.91966 91.89329 90.66767 assigned negative charge : -301.9702 centred at (gu) : 87.36824 91.54168 90.90109 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 81706 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17075 grid for indexing accessible points = 1.400000 m= 35963 mr = 58399 m= 8380 mr = 28014 m= 994 mr = 6050 m= 54 mr = 589 m= 0 mr = 20 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 34025 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 43 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 15214 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) : 0.7431995 object centre at (A) : 48.99700 5.035501 25.19550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9019175E-02 3.0832093E-02 midg,1,midg; midg,igrid,midg 5.2818999E-02 0.1090987 1,midg,midg; igrid,midg,midg 6.0042918E-02 -5.1407222E-02 gauss-seidel spectral radius is 0.9989235 estimated iterations to convergence 241 setup time was (sec) 0.9800000 now iterating at: 05:25:56 rms-change max change #iterations 4.901520 167.9716 at 10iterations 2.501118 74.44904 at 20iterations 1.281495 37.28004 at 30iterations 0.6515295 18.67642 at 40iterations 0.3333049 9.656981 at 50iterations 0.1705417 5.153878 at 60iterations 8.6789131E-02 2.488617 at 70iterations 4.4570062E-02 1.219437 at 80iterations 2.2963850E-02 0.6256895 at 90iterations 1.1850460E-02 0.3118486 at 100iterations 6.1590751E-03 0.1876678 at 110iterations 3.2628549E-03 8.9690208E-02 at 120iterations finished qdiffx linear iterations at : 05:26:03 total time elapsed so far: 8.080000 # loops : 120 mean,max change (kT/e) : 3.2628549E-03 8.9690208E-02 energy calculations done at 8.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.280000 DelPhi exited at 05:26:04 8.279u 0.234s 0:08.91 95.3% 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 05:26:04 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2189 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.344398 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): 25.70500 72.28900 ymin,ymax (A): -18.91500 28.98600 zmin,zma (A): 3.944000 46.44700 x,y,z range (A): 46.58400 47.90100 42.50300 scale (grids/A): 3.344398 object centre (A): 48.99700 5.035501 25.19550 number of atom coordinates read : 2189 total number of charged atoms : 1910 net assigned charge : 7.500009 assigned positive charge : 309.4701 centred at (gu) : 85.37955 92.83997 91.00141 assigned negative charge : -301.9702 centred at (gu) : 86.05234 92.31258 91.35172 start vw surface at 0.1500000 fill in re-entrant regions at 0.9200000 boundary points on vw surface= 187823 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17075 grid for indexing accessible points = 1.400000 m= 108057 mr = 139842 m= 49249 mr = 91237 m= 16400 mr = 41520 m= 4081 mr = 13345 m= 697 mr = 3194 m= 61 mr = 505 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.150000 number of dielectric boundary points 76686 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.300000 number of grid points assigned charge 15280 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) : 2.229599 object centre at (A) : 48.99700 5.035501 25.19550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1470395 0.2368872 midg,1,midg; midg,igrid,midg 0.3795993 0.7922086 1,midg,midg; igrid,midg,midg 0.5020527 -0.5668095 gauss-seidel spectral radius is 0.9993212 estimated iterations to convergence 303 setup time was (sec) 2.480000 now iterating at: 05:26:07 rms-change max change #iterations 10.69078 326.3542 at 10iterations 6.401009 122.0358 at 20iterations 3.821525 71.08538 at 30iterations 2.277556 41.51999 at 40iterations 1.357472 22.87147 at 50iterations 0.8029628 12.89230 at 60iterations 0.4764945 7.892340 at 70iterations 0.2824491 4.743988 at 80iterations 0.1672148 2.900976 at 90iterations 9.8861091E-02 1.594543 at 100iterations 5.8621731E-02 1.004172 at 110iterations 3.4868374E-02 0.5710583 at 120iterations 2.0848598E-02 0.3582649 at 130iterations 1.2667835E-02 0.2301159 at 140iterations 7.8515243E-03 0.1319122 at 150iterations 5.0412617E-03 9.0257645E-02 at 160iterations 3.4264512E-03 5.9753418E-02 at 170iterations 2.4807935E-03 4.2438507E-02 at 180iterations finished qdiffx linear iterations at : 05:26:18 total time elapsed so far: 13.89000 # loops : 180 mean,max change (kT/e) : 2.4807935E-03 4.2438507E-02 energy calculations done at 13.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.08000 DelPhi exited at 05:26:19 14.082u 0.250s 0:14.61 98.0% 0+0k 0+0io 0pf+0w