Sun Oct 9 21:08:37 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 Sun Oct 9 2011 at 21:08:37 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2576 !!! WARNING: SEP 142 has a net charge of -0.4750 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: 0.6387598 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): 10.45600 66.18900 ymin,ymax (A): -11.95400 37.01000 zmin,zma (A): -11.75300 41.21700 x,y,z range (A): 55.73300 48.96400 52.97000 scale (grids/A): 0.6387598 object centre (A): 38.32250 12.52800 14.73200 number of atom coordinates read : 2576 total number of charged atoms : 2430 net assigned charge : 4.525009 assigned positive charge : 389.2179 centred at (gu) : 90.58762 91.13723 90.14451 assigned negative charge : -384.6936 centred at (gu) : 90.64217 91.08499 90.18120 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6877 nv = 96 ne = 84 npr = 51926 no. pairs analyzed = 51926 no. exposed pairs = 3064 no. arc points = 21847 no. surface atoms = 1035 nbur = 1541 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 344 mr = 3753 m= 0 mr = 31 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 102 time to turn everything in is 0.2100000 number of dielectric boundary points 3437 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2191 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8412 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0090440E-08 2.2710385E-09 midg,1,midg; midg,igrid,midg 4.2468321E-10 1.5462025E-08 1,midg,midg; igrid,midg,midg 1.0928502E-08 1.7356105E-10 gauss-seidel spectral radius is 0.9873005 estimated iterations to convergence 73 setup time was (sec) 0.4000000 now iterating at: 21:08:37 rms-change max change #iterations 0.1461681 22.50354 at 10iterations 1.4507994E-02 2.255463 at 20iterations 1.4176562E-03 0.1977997 at 30iterations 1.3985475E-04 2.1144867E-02 at 40iterations 1.4153497E-05 1.9731522E-03 at 50iterations finished qdiffx linear iterations at : 21:08:40 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.4153497E-05 1.9731522E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 21:08:40 3.416u 0.163s 0:03.84 92.9% 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 Sun Oct 9 2011 at 21:08:40 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2576 !!! WARNING: SEP 142 has a net charge of -0.4750 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: 1.916279 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): 10.45600 66.18900 ymin,ymax (A): -11.95400 37.01000 zmin,zma (A): -11.75300 41.21700 x,y,z range (A): 55.73300 48.96400 52.97000 scale (grids/A): 1.916279 object centre (A): 38.32250 12.52800 14.73200 number of atom coordinates read : 2576 total number of charged atoms : 2430 net assigned charge : 4.525009 assigned positive charge : 389.2179 centred at (gu) : 91.76246 93.41112 90.43287 assigned negative charge : -384.6936 centred at (gu) : 91.92612 93.25488 90.54343 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 75047 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21847 grid for indexing accessible points = 1.400000 m= 25305 mr = 51888 m= 3764 mr = 18370 m= 240 mr = 2371 m= 3 mr = 114 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 1758 time to turn everything in is 0.3700000 number of dielectric boundary points 31616 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 141 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 19147 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) : 0.6387598 object centre at (A) : 38.32250 12.52800 14.73200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3548651E-02 -8.9273164E-03 midg,1,midg; midg,igrid,midg -1.3568110E-02 8.1248833E-03 1,midg,midg; igrid,midg,midg 1.4104328E-02 3.0597124E-02 gauss-seidel spectral radius is 0.9986429 estimated iterations to convergence 215 setup time was (sec) 0.5800000 now iterating at: 21:08:41 rms-change max change #iterations 4.231441 178.0194 at 10iterations 1.983247 74.54274 at 20iterations 0.9305487 30.91583 at 30iterations 0.4357716 12.70275 at 40iterations 0.2043732 7.162963 at 50iterations 9.6257746E-02 2.991325 at 60iterations 4.4916227E-02 1.334496 at 70iterations 2.1117743E-02 0.6201973 at 80iterations 9.9201752E-03 0.2929688 at 90iterations 4.6491041E-03 0.1478271 at 100iterations 2.1884285E-03 7.0102692E-02 at 110iterations 1.0240035E-03 3.4086227E-02 at 120iterations finished qdiffx linear iterations at : 21:08:48 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 1.0240035E-03 3.4086227E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 21:08:49 7.803u 0.187s 0:08.33 95.7% 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 Sun Oct 9 2011 at 21:08:49 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2576 !!! WARNING: SEP 142 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.874419 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): 10.45600 66.18900 ymin,ymax (A): -11.95400 37.01000 zmin,zma (A): -11.75300 41.21700 x,y,z range (A): 55.73300 48.96400 52.97000 scale (grids/A): 2.874419 object centre (A): 38.32250 12.52800 14.73200 number of atom coordinates read : 2576 total number of charged atoms : 2430 net assigned charge : 4.525009 assigned positive charge : 389.2179 centred at (gu) : 92.64359 95.11662 90.64923 assigned negative charge : -384.6936 centred at (gu) : 92.88923 94.88211 90.81519 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 173690 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21847 grid for indexing accessible points = 1.400000 m= 83578 mr = 125400 m= 28312 mr = 68291 m= 6659 mr = 22329 m= 1073 mr = 5101 m= 56 mr = 774 m= 0 mr = 23 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 5895 time to turn everything in is 0.9300000 number of dielectric boundary points 71450 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 19440 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) : 1.916279 object centre at (A) : 38.32250 12.52800 14.73200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2230828 -0.2375847 midg,1,midg; midg,igrid,midg -0.2486426 0.1142527 1,midg,midg; igrid,midg,midg 0.2652800 0.2762405 gauss-seidel spectral radius is 0.9992593 estimated iterations to convergence 290 setup time was (sec) 1.170000 now iterating at: 21:08:50 rms-change max change #iterations 9.889415 369.8324 at 10iterations 5.728804 115.5067 at 20iterations 3.308761 61.25462 at 30iterations 1.904344 34.21121 at 40iterations 1.094898 22.69563 at 50iterations 0.6299516 11.43829 at 60iterations 0.3614745 6.403990 at 70iterations 0.2076316 3.728103 at 80iterations 0.1194001 2.251163 at 90iterations 6.8458982E-02 1.286366 at 100iterations 3.9250307E-02 0.7217417 at 110iterations 2.2492779E-02 0.3958137 at 120iterations 1.2915761E-02 0.2239609 at 130iterations 7.4088816E-03 0.1352558 at 140iterations 4.2535844E-03 7.6733589E-02 at 150iterations 2.4373226E-03 4.4555664E-02 at 160iterations 1.4014811E-03 2.6992798E-02 at 170iterations 8.0467650E-04 1.4189720E-02 at 180iterations finished qdiffx linear iterations at : 21:09:01 total time elapsed so far: 12.46000 # loops : 180 mean,max change (kT/e) : 8.0467650E-04 1.4189720E-02 energy calculations done at 12.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.60000 DelPhi exited at 21:09:02 12.604u 0.210s 0:13.08 97.9% 0+0k 0+0io 0pf+0w