Tue Oct 11 07:30:44 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 07:30:44 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3262 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5878565 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): 0.8149999 49.15100 ymin,ymax (A): -7.427000 48.96000 zmin,zma (A): 0.8219999 61.38100 x,y,z range (A): 48.33600 56.38700 60.55900 scale (grids/A): 0.5878565 object centre (A): 24.98300 20.76650 31.10150 number of atom coordinates read : 3262 total number of charged atoms : 3096 net assigned charge : -9.9990189E-02 assigned positive charge : 488.9368 centred at (gu) : 89.58902 89.19787 90.82365 assigned negative charge : -489.0379 centred at (gu) : 89.50291 89.10538 90.75948 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7492 nv = 96 ne = 84 npr = 67010 no. pairs analyzed = 67010 no. exposed pairs = 3824 no. arc points = 26287 no. surface atoms = 1301 nbur = 1961 mkacc time = 0.1600000 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 = 1.456000 m= 320 mr = 4336 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 37 time to turn everything in is 0.3800000 number of dielectric boundary points 3441 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2668 ## 267 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9361 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6720376E-09 2.4147944E-09 midg,1,midg; midg,igrid,midg -3.5429801E-09 2.3666058E-09 1,midg,midg; igrid,midg,midg -3.0045175E-09 2.4160760E-09 gauss-seidel spectral radius is 0.9850793 estimated iterations to convergence 67 setup time was (sec) 0.6200000 now iterating at: 07:30:45 rms-change max change #iterations 0.1129117 16.54887 at 10iterations 1.0078651E-02 1.354034 at 20iterations 1.2696193E-03 0.2120190 at 30iterations 3.0880957E-04 6.1061859E-02 at 40iterations 8.5957588E-05 1.7330170E-02 at 50iterations finished qdiffx linear iterations at : 07:30:48 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 8.5957588E-05 1.7330170E-02 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 07:30:49 3.585u 0.195s 0:04.32 87.2% 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 07:30:49 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3262 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.763569 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): 0.8149999 49.15100 ymin,ymax (A): -7.427000 48.96000 zmin,zma (A): 0.8219999 61.38100 x,y,z range (A): 48.33600 56.38700 60.55900 scale (grids/A): 1.763569 object centre (A): 24.98300 20.76650 31.10150 number of atom coordinates read : 3262 total number of charged atoms : 3096 net assigned charge : -9.9990189E-02 assigned positive charge : 488.9368 centred at (gu) : 88.76611 87.59278 92.47035 assigned negative charge : -489.0379 centred at (gu) : 88.50832 87.31573 92.27789 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 81613 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26287 grid for indexing accessible points = 1.400000 m= 29751 mr = 58517 m= 3981 mr = 22686 m= 138 mr = 2536 m= 0 mr = 34 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1970 time to turn everything in is 0.6200000 number of dielectric boundary points 31710 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 252 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 24145 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) : 0.5878565 object centre at (A) : 24.98300 20.76650 31.10150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.8886367E-03 2.1428026E-03 midg,1,midg; midg,igrid,midg -1.8859463E-02 7.2857141E-03 1,midg,midg; igrid,midg,midg -1.2097522E-02 1.0790830E-02 gauss-seidel spectral radius is 0.9984756 estimated iterations to convergence 203 setup time was (sec) 0.9300000 now iterating at: 07:30:50 rms-change max change #iterations 4.132854 151.9431 at 10iterations 1.850156 57.28330 at 20iterations 0.8312038 28.11511 at 30iterations 0.3750671 11.23849 at 40iterations 0.1684563 4.884289 at 50iterations 7.6095782E-02 2.392918 at 60iterations 3.4374986E-02 1.026672 at 70iterations 1.5497115E-02 0.5463486 at 80iterations 7.0677609E-03 0.2385263 at 90iterations 3.2706654E-03 0.1019135 at 100iterations 1.5369481E-03 5.0313950E-02 at 110iterations 7.4299355E-04 2.7374268E-02 at 120iterations finished qdiffx linear iterations at : 07:30:57 total time elapsed so far: 7.900000 # loops : 120 mean,max change (kT/e) : 7.4299355E-04 2.7374268E-02 energy calculations done at 7.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.090000 DelPhi exited at 07:30:57 8.088u 0.245s 0:08.62 96.5% 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 07:30:57 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3262 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.645354 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): 0.8149999 49.15100 ymin,ymax (A): -7.427000 48.96000 zmin,zma (A): 0.8219999 61.38100 x,y,z range (A): 48.33600 56.38700 60.55900 scale (grids/A): 2.645354 object centre (A): 24.98300 20.76650 31.10150 number of atom coordinates read : 3262 total number of charged atoms : 3096 net assigned charge : -9.9990189E-02 assigned positive charge : 488.9368 centred at (gu) : 88.14881 86.38889 93.70547 assigned negative charge : -489.0379 centred at (gu) : 87.76228 85.97341 93.41671 start vw surface at 0.2000000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 188662 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26287 grid for indexing accessible points = 1.400000 m= 97496 mr = 140902 m= 34147 mr = 81555 m= 6949 mr = 28120 m= 719 mr = 5317 m= 33 mr = 444 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 6495 time to turn everything in is 1.580000 number of dielectric boundary points 71652 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 24761 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) : 1.763569 object centre at (A) : 24.98300 20.76650 31.10150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2793843 -0.2771517 midg,1,midg; midg,igrid,midg -0.3381017 5.1623855E-02 1,midg,midg; igrid,midg,midg -0.1288960 0.1363019 gauss-seidel spectral radius is 0.9992226 estimated iterations to convergence 283 setup time was (sec) 1.910000 now iterating at: 07:30:59 rms-change max change #iterations 10.06034 270.6957 at 10iterations 5.755196 110.4823 at 20iterations 3.285159 59.10547 at 30iterations 1.872499 38.63336 at 40iterations 1.065911 19.05878 at 50iterations 0.6060621 11.78624 at 60iterations 0.3440470 6.896614 at 70iterations 0.1956521 3.431385 at 80iterations 0.1107766 1.846159 at 90iterations 6.2964469E-02 1.245159 at 100iterations 3.5701156E-02 0.6330080 at 110iterations 2.0254495E-02 0.3542290 at 120iterations 1.1512685E-02 0.2270432 at 130iterations 6.5557514E-03 0.1107159 at 140iterations 3.7377940E-03 6.9977760E-02 at 150iterations 2.1505558E-03 3.9470673E-02 at 160iterations 1.2448264E-03 2.1949768E-02 at 170iterations 7.3500484E-04 1.4484406E-02 at 180iterations finished qdiffx linear iterations at : 07:31:11 total time elapsed so far: 13.03000 # loops : 180 mean,max change (kT/e) : 7.3500484E-04 1.4484406E-02 energy calculations done at 13.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.22000 DelPhi exited at 07:31:11 13.217u 0.230s 0:13.78 97.5% 0+0k 0+0io 0pf+0w