Sat Oct 15 14:41:22 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+sph.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 = amb.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 Sat Oct 15 2011 at 14:41:22 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 !!! 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: 0.5315496 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): -18.69800 48.27600 ymin,ymax (A): -28.00600 19.74300 zmin,zma (A): -42.08000 8.813000 x,y,z range (A): 66.97400 47.74900 50.89300 scale (grids/A): 0.5315496 object centre (A): 14.78900 -4.131500 -16.63350 number of atom coordinates read : 3036 total number of charged atoms : 2895 net assigned charge : 2.2567809E-05 assigned positive charge : 452.0899 centred at (gu) : 88.85998 89.41807 88.99960 assigned negative charge : -452.0911 centred at (gu) : 88.85693 89.30287 88.87521 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5575 nv = 96 ne = 84 npr = 60005 no. pairs analyzed = 60005 no. exposed pairs = 4167 no. arc points = 29459 no. surface atoms = 1386 nbur = 1650 mkacc time = 9.9999994E-02 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 = 1.624000 m= 218 mr = 2676 m= 0 mr = 9 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 3108 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2940 ## 424 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7389 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.2256278E-10 3.7355957E-10 midg,1,midg; midg,igrid,midg -5.1554172E-10 3.8598993E-10 1,midg,midg; igrid,midg,midg -3.6924391E-12 1.5580997E-11 gauss-seidel spectral radius is 0.9817753 estimated iterations to convergence 61 setup time was (sec) 0.3900000 now iterating at: 14:41:23 rms-change max change #iterations 6.1248522E-02 10.69523 at 10iterations 3.9180801E-03 0.7629718 at 20iterations 2.3971818E-04 3.7225723E-02 at 30iterations 1.5238909E-05 2.6130676E-03 at 40iterations 1.1406913E-06 2.2125244E-04 at 50iterations finished qdiffx linear iterations at : 14:41:26 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 1.1406913E-06 2.2125244E-04 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 14:41:27 3.513u 0.241s 0:05.26 71.2% 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 Sat Oct 15 2011 at 14:41:28 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 !!! 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: 1.594649 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): -18.69800 48.27600 ymin,ymax (A): -28.00600 19.74300 zmin,zma (A): -42.08000 8.813000 x,y,z range (A): 66.97400 47.74900 50.89300 scale (grids/A): 1.594649 object centre (A): 14.78900 -4.131500 -16.63350 number of atom coordinates read : 3036 total number of charged atoms : 2895 net assigned charge : 2.2567809E-05 assigned positive charge : 452.0899 centred at (gu) : 86.57907 88.25325 86.99821 assigned negative charge : -452.0911 centred at (gu) : 86.57013 87.90821 86.62537 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 62054 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29459 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 17487 mr = 40097 m= 1533 mr = 11269 m= 37 mr = 643 m= 0 mr = 2 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 423 time to turn everything in is 0.3000000 number of dielectric boundary points 29100 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 352 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 22038 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) : 0.5315496 object centre at (A) : 14.78900 -4.131500 -16.63350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7418675E-02 3.5796671E-03 midg,1,midg; midg,igrid,midg -3.2889983E-03 4.8419330E-03 1,midg,midg; igrid,midg,midg -5.6836900E-04 1.3937358E-03 gauss-seidel spectral radius is 0.9981021 estimated iterations to convergence 182 setup time was (sec) 0.5300000 now iterating at: 14:41:30 rms-change max change #iterations 3.141136 138.2466 at 10iterations 1.275311 50.86491 at 20iterations 0.5206650 23.44417 at 30iterations 0.2123035 8.168267 at 40iterations 8.6518973E-02 3.172590 at 50iterations 3.5391308E-02 1.344773 at 60iterations 1.4390302E-02 0.5501201 at 70iterations 5.8705416E-03 0.2496223 at 80iterations 2.4028267E-03 9.6854210E-02 at 90iterations 9.7959943E-04 3.5916328E-02 at 100iterations 4.0110061E-04 1.4984131E-02 at 110iterations 1.6404479E-04 5.9523582E-03 at 120iterations finished qdiffx linear iterations at : 14:41:45 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 1.6404479E-04 5.9523582E-03 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 14:41:46 7.970u 0.255s 0:17.70 46.4% 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 Sat Oct 15 2011 at 14:41:46 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 !!! 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: 2.391973 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): -18.69800 48.27600 ymin,ymax (A): -28.00600 19.74300 zmin,zma (A): -42.08000 8.813000 x,y,z range (A): 66.97400 47.74900 50.89300 scale (grids/A): 2.391973 object centre (A): 14.78900 -4.131500 -16.63350 number of atom coordinates read : 3036 total number of charged atoms : 2895 net assigned charge : 2.2567809E-05 assigned positive charge : 452.0899 centred at (gu) : 84.86832 87.37968 85.49708 assigned negative charge : -452.0911 centred at (gu) : 84.85514 86.86217 84.93794 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 143960 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29459 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 62018 mr = 98686 m= 15953 mr = 47123 m= 2169 mr = 11407 m= 107 mr = 1244 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 1443 time to turn everything in is 0.7800000 number of dielectric boundary points 65714 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 31 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 23112 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) : 1.594649 object centre at (A) : 14.78900 -4.131500 -16.63350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2817693 6.3576072E-02 midg,1,midg; midg,igrid,midg -3.8448159E-02 6.3895233E-02 1,midg,midg; igrid,midg,midg -0.2367038 0.1445991 gauss-seidel spectral radius is 0.9991147 estimated iterations to convergence 266 setup time was (sec) 1.050000 now iterating at: 14:41:49 rms-change max change #iterations 8.382628 279.4190 at 10iterations 4.658810 122.4305 at 20iterations 2.569527 64.65709 at 30iterations 1.415830 33.59007 at 40iterations 0.7777594 18.49822 at 50iterations 0.4248952 10.11252 at 60iterations 0.2321897 5.120040 at 70iterations 0.1265644 3.028550 at 80iterations 6.9114476E-02 1.531221 at 90iterations 3.7658904E-02 0.7899590 at 100iterations 2.0472696E-02 0.4427814 at 110iterations 1.1195229E-02 0.2481179 at 120iterations 6.0725105E-03 0.1337166 at 130iterations 3.3097297E-03 8.0352783E-02 at 140iterations 1.8012172E-03 3.7940979E-02 at 150iterations 9.8051713E-04 2.3475647E-02 at 160iterations 5.3461804E-04 1.1722565E-02 at 170iterations 2.9034680E-04 6.6196918E-03 at 180iterations finished qdiffx linear iterations at : 14:42:11 total time elapsed so far: 13.07000 # loops : 180 mean,max change (kT/e) : 2.9034680E-04 6.6196918E-03 energy calculations done at 13.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.20000 DelPhi exited at 14:42:12 13.203u 0.271s 0:25.77 52.2% 0+0k 0+0io 0pf+0w