Sat Oct 8 22:02:27 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 Sat Oct 8 2011 at 22:02:28 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2319 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 0.6025320 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): -26.93600 27.56200 ymin,ymax (A): 7.610000 49.01300 zmin,zma (A): -15.06000 44.02400 x,y,z range (A): 54.49800 41.40300 59.08400 scale (grids/A): 0.6025320 object centre (A): 0.3129997 28.31150 14.48200 number of atom coordinates read : 2319 total number of charged atoms : 2184 net assigned charge : 10.51402 assigned positive charge : 339.9425 centred at (gu) : 90.48462 91.09184 91.48789 assigned negative charge : -329.4291 centred at (gu) : 90.47362 91.02335 91.48743 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5792 nv = 96 ne = 84 npr = 46039 no. pairs analyzed = 46039 no. exposed pairs = 3144 no. arc points = 22754 no. surface atoms = 1047 nbur = 1272 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 298 mr = 2885 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3192 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2297 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7056 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4963386E-09 6.7429808E-09 midg,1,midg; midg,igrid,midg 2.0257123E-09 9.0758219E-09 1,midg,midg; igrid,midg,midg 4.0273505E-09 5.7939276E-09 gauss-seidel spectral radius is 0.9857299 estimated iterations to convergence 69 setup time was (sec) 0.3800000 now iterating at: 22:02:28 rms-change max change #iterations 0.1015537 16.03779 at 10iterations 8.7812264E-03 1.637393 at 20iterations 7.4808236E-04 0.1210222 at 30iterations 6.3221931E-05 1.0512352E-02 at 40iterations 5.7135480E-06 8.8214874E-04 at 50iterations finished qdiffx linear iterations at : 22:02:31 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 5.7135480E-06 8.8214874E-04 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 22:02:31 3.345u 0.166s 0:03.78 92.5% 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 Sat Oct 8 2011 at 22:02:31 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2319 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 1.807596 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): -26.93600 27.56200 ymin,ymax (A): 7.610000 49.01300 zmin,zma (A): -15.06000 44.02400 x,y,z range (A): 54.49800 41.40300 59.08400 scale (grids/A): 1.807596 object centre (A): 0.3129997 28.31150 14.48200 number of atom coordinates read : 2319 total number of charged atoms : 2184 net assigned charge : 10.51402 assigned positive charge : 339.9425 centred at (gu) : 91.45351 93.27524 94.46339 assigned negative charge : -329.4291 centred at (gu) : 91.42097 93.07014 94.46227 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 62354 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22754 grid for indexing accessible points = 1.400000 m= 21130 mr = 40996 m= 3048 mr = 14633 m= 147 mr = 1733 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 29303 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 234 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 17065 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) : 0.6025320 object centre at (A) : 0.3129997 28.31150 14.48200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7735066E-02 1.8590990E-02 midg,1,midg; midg,igrid,midg -3.8648972E-03 1.8270170E-02 1,midg,midg; igrid,midg,midg 2.8918236E-02 3.0079421E-02 gauss-seidel spectral radius is 0.9984680 estimated iterations to convergence 203 setup time was (sec) 0.5200000 now iterating at: 22:02:32 rms-change max change #iterations 3.577641 167.3990 at 10iterations 1.586930 57.54605 at 20iterations 0.7039046 26.88675 at 30iterations 0.3158982 11.51492 at 40iterations 0.1409611 5.604806 at 50iterations 6.2996693E-02 2.197417 at 60iterations 2.8096320E-02 0.9992971 at 70iterations 1.2552822E-02 0.4837742 at 80iterations 5.6172530E-03 0.1982307 at 90iterations 2.5164383E-03 8.8806152E-02 at 100iterations 1.1254734E-03 3.8662434E-02 at 110iterations 5.0143362E-04 1.8764019E-02 at 120iterations finished qdiffx linear iterations at : 22:02:39 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 5.0143362E-04 1.8764019E-02 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.640000 DelPhi exited at 22:02:39 7.647u 0.203s 0:08.12 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 Sat Oct 8 2011 at 22:02:39 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2319 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 2.711394 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): -26.93600 27.56200 ymin,ymax (A): 7.610000 49.01300 zmin,zma (A): -15.06000 44.02400 x,y,z range (A): 54.49800 41.40300 59.08400 scale (grids/A): 2.711394 object centre (A): 0.3129997 28.31150 14.48200 number of atom coordinates read : 2319 total number of charged atoms : 2184 net assigned charge : 10.51402 assigned positive charge : 339.9425 centred at (gu) : 92.18025 94.91273 96.69501 assigned negative charge : -329.4291 centred at (gu) : 92.13149 94.60520 96.69344 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 144071 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22754 grid for indexing accessible points = 1.400000 m= 68985 mr = 99983 m= 23727 mr = 54377 m= 5284 mr = 18275 m= 608 mr = 3706 m= 13 mr = 339 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7700000 number of dielectric boundary points 66008 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 17469 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) : 1.807596 object centre at (A) : 0.3129997 28.31150 14.48200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4009487 0.1828415 midg,1,midg; midg,igrid,midg -6.1685629E-02 0.2080287 1,midg,midg; igrid,midg,midg 0.3813366 0.3312291 gauss-seidel spectral radius is 0.9992163 estimated iterations to convergence 282 setup time was (sec) 1.010000 now iterating at: 22:02:41 rms-change max change #iterations 8.701824 323.6861 at 10iterations 5.044351 126.6900 at 20iterations 2.904466 68.66223 at 30iterations 1.664810 41.47341 at 40iterations 0.9516276 23.25260 at 50iterations 0.5420841 11.29488 at 60iterations 0.3082794 7.676348 at 70iterations 0.1746422 3.482877 at 80iterations 9.8825440E-02 1.938831 at 90iterations 5.6075748E-02 1.171851 at 100iterations 3.1753317E-02 0.6757851 at 110iterations 1.7923141E-02 0.3617750 at 120iterations 1.0133558E-02 0.1962070 at 130iterations 5.7256771E-03 0.1196404 at 140iterations 3.2397767E-03 6.5973282E-02 at 150iterations 1.8279025E-03 3.7051797E-02 at 160iterations 1.0306647E-03 1.9932747E-02 at 170iterations 5.8288412E-04 1.3099670E-02 at 180iterations finished qdiffx linear iterations at : 22:02:52 total time elapsed so far: 12.20000 # loops : 180 mean,max change (kT/e) : 5.8288412E-04 1.3099670E-02 energy calculations done at 12.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.34000 DelPhi exited at 22:02:52 12.342u 0.208s 0:12.82 97.8% 0+0k 0+0io 0pf+0w