Wed Feb 15 08:54:36 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:54:36 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: MG4 458 has a net charge of 2.0000 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: 0.5937192 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): 21.49900 70.16200 ymin,ymax (A): -26.47500 33.48600 zmin,zma (A): -6.753000 46.02100 x,y,z range (A): 48.66300 59.96100 52.77400 scale (grids/A): 0.5937192 object centre (A): 45.83050 3.505500 19.63400 number of atom coordinates read : 2606 total number of charged atoms : 2463 net assigned charge : 11.00002 assigned positive charge : 395.5995 centred at (gu) : 88.96926 89.67421 90.53307 assigned negative charge : -384.6004 centred at (gu) : 88.87899 89.60804 90.60934 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6022 nv = 96 ne = 84 npr = 52141 no. pairs analyzed = 52141 no. exposed pairs = 3519 no. arc points = 25335 no. surface atoms = 1167 nbur = 1439 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 306 mr = 2986 m= 4 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3323 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2595 ## 294 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 7682 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.4318070E-09 1.7855575E-09 midg,1,midg; midg,igrid,midg 2.0397566E-09 5.4179190E-09 1,midg,midg; igrid,midg,midg 1.4391102E-09 5.1796554E-09 gauss-seidel spectral radius is 0.9853269 estimated iterations to convergence 68 setup time was (sec) 0.4300000 now iterating at: 08:54:38 rms-change max change #iterations 0.1028191 17.80956 at 10iterations 8.3775530E-03 1.511095 at 20iterations 6.9799373E-04 0.1154327 at 30iterations 5.8947608E-05 9.6683502E-03 at 40iterations 5.0382605E-06 8.2015991E-04 at 50iterations finished qdiffx linear iterations at : 08:54:42 total time elapsed so far: 4.590000 # loops : 50 mean,max change (kT/e) : 5.0382605E-06 8.2015991E-04 energy calculations done at 4.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.720000 DelPhi exited at 08:54:43 4.728u 0.306s 0:06.85 73.2% 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 Wed Feb 15 2012 at 08:54:43 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: MG4 458 has a net charge of 2.0000 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: 1.781158 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): 21.49900 70.16200 ymin,ymax (A): -26.47500 33.48600 zmin,zma (A): -6.753000 46.02100 x,y,z range (A): 48.66300 59.96100 52.77400 scale (grids/A): 1.781158 object centre (A): 45.83050 3.505500 19.63400 number of atom coordinates read : 2606 total number of charged atoms : 2463 net assigned charge : 11.00002 assigned positive charge : 395.5995 centred at (gu) : 86.90699 89.02188 91.59895 assigned negative charge : -384.6004 centred at (gu) : 86.63676 88.82386 91.82795 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 65774 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25335 grid for indexing accessible points = 1.400000 m= 21418 mr = 42916 m= 2651 mr = 14893 m= 110 mr = 1371 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 180 time to turn everything in is 0.3600000 number of dielectric boundary points 30748 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 271 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 19177 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) : 0.5937192 object centre at (A) : 45.83050 3.505500 19.63400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4449968E-02 1.3223948E-03 midg,1,midg; midg,igrid,midg 3.2787140E-02 2.9902589E-02 1,midg,midg; igrid,midg,midg 5.4142540E-03 2.1729846E-02 gauss-seidel spectral radius is 0.9984493 estimated iterations to convergence 201 setup time was (sec) 0.6400000 now iterating at: 08:54:44 rms-change max change #iterations 3.703454 175.9027 at 10iterations 1.639045 70.89375 at 20iterations 0.7279446 25.32853 at 30iterations 0.3242614 11.47799 at 40iterations 0.1443826 5.046488 at 50iterations 6.4115614E-02 2.228096 at 60iterations 2.8546255E-02 1.012100 at 70iterations 1.2718383E-02 0.4702148 at 80iterations 5.6637721E-03 0.2087498 at 90iterations 2.5237035E-03 8.3890915E-02 at 100iterations 1.1254488E-03 4.0388107E-02 at 110iterations 4.9963058E-04 1.6989708E-02 at 120iterations finished qdiffx linear iterations at : 08:54:53 total time elapsed so far: 9.580000 # loops : 120 mean,max change (kT/e) : 4.9963058E-04 1.6989708E-02 energy calculations done at 9.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.710000 DelPhi exited at 08:54:55 9.716u 0.328s 0:12.27 81.7% 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 Wed Feb 15 2012 at 08:54:56 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: MG4 458 has a net charge of 2.0000 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: 2.671737 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): 21.49900 70.16200 ymin,ymax (A): -26.47500 33.48600 zmin,zma (A): -6.753000 46.02100 x,y,z range (A): 48.66300 59.96100 52.77400 scale (grids/A): 2.671737 object centre (A): 45.83050 3.505500 19.63400 number of atom coordinates read : 2606 total number of charged atoms : 2463 net assigned charge : 11.00002 assigned positive charge : 395.5995 centred at (gu) : 85.36033 88.53260 92.39822 assigned negative charge : -384.6004 centred at (gu) : 84.95503 88.23573 92.74185 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 152126 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25335 grid for indexing accessible points = 1.400000 m= 71250 mr = 104663 m= 22664 mr = 56267 m= 4376 mr = 17331 m= 465 mr = 2962 m= 25 mr = 249 m= 0 mr = 8 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 669 time to turn everything in is 0.8300000 number of dielectric boundary points 69426 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 19700 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) : 1.781158 object centre at (A) : 45.83050 3.505500 19.63400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1334793 -1.0968440E-02 midg,1,midg; midg,igrid,midg 0.2854700 0.5235497 1,midg,midg; igrid,midg,midg 4.8765104E-02 0.2325487 gauss-seidel spectral radius is 0.9992147 estimated iterations to convergence 282 setup time was (sec) 1.110000 now iterating at: 08:54:58 rms-change max change #iterations 9.076327 296.1423 at 10iterations 5.231699 133.7755 at 20iterations 2.991200 64.88206 at 30iterations 1.698064 32.93637 at 40iterations 0.9644907 20.43374 at 50iterations 0.5456501 11.59994 at 60iterations 0.3087028 6.292725 at 70iterations 0.1743364 3.529041 at 80iterations 9.8389372E-02 1.954985 at 90iterations 5.5632487E-02 1.052567 at 100iterations 3.1400856E-02 0.6126671 at 110iterations 1.7732816E-02 0.3913517 at 120iterations 9.9900253E-03 0.2081909 at 130iterations 5.6407927E-03 0.1123238 at 140iterations 3.1848003E-03 6.4521790E-02 at 150iterations 1.7894723E-03 3.8293839E-02 at 160iterations 1.0120192E-03 2.0288467E-02 at 170iterations 5.7201908E-04 1.0860443E-02 at 180iterations finished qdiffx linear iterations at : 08:55:13 total time elapsed so far: 16.41000 # loops : 180 mean,max change (kT/e) : 5.7201908E-04 1.0860443E-02 energy calculations done at 16.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.55000 DelPhi exited at 08:55:13 16.552u 0.279s 0:17.37 96.8% 0+0k 0+0io 0pf+0w