Tue Oct 11 03:44:43 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 Tue Oct 11 2011 at 03:44:43 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 # of charge parameter records: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2787 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6513347 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): -7.086000 44.47600 ymin,ymax (A): 27.36600 82.02299 zmin,zma (A): -27.99300 24.39800 x,y,z range (A): 51.56200 54.65700 52.39100 scale (grids/A): 0.6513347 object centre (A): 18.69500 54.69450 -1.797501 number of atom coordinates read : 2787 total number of charged atoms : 2676 net assigned charge : 3.162015 assigned positive charge : 427.5065 centred at (gu) : 89.40298 89.05405 90.98083 assigned negative charge : -424.3452 centred at (gu) : 89.35935 88.94213 90.69169 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7988 nv = 96 ne = 84 npr = 54493 no. pairs analyzed = 54493 no. exposed pairs = 3603 no. arc points = 25289 no. surface atoms = 1213 nbur = 1574 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 459 mr = 4361 m= 1 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.2000000 number of dielectric boundary points 4029 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2406 ## 242 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 9530 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.6681147E-08 6.7234993E-08 midg,1,midg; midg,igrid,midg -1.6545041E-08 2.0647002E-08 1,midg,midg; igrid,midg,midg -1.6829894E-09 1.2021450E-08 gauss-seidel spectral radius is 0.9878044 estimated iterations to convergence 74 setup time was (sec) 0.4000000 now iterating at: 03:44:44 rms-change max change #iterations 0.1641965 24.54947 at 10iterations 1.7135294E-02 2.267900 at 20iterations 1.8374429E-03 0.3017454 at 30iterations 2.1866664E-04 3.0977249E-02 at 40iterations 3.5596066E-05 7.0629120E-03 at 50iterations finished qdiffx linear iterations at : 03:44:47 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 3.5596066E-05 7.0629120E-03 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 03:44:47 3.348u 0.164s 0:03.94 88.8% 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 03:44:47 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2787 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.954004 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): -7.086000 44.47600 ymin,ymax (A): 27.36600 82.02299 zmin,zma (A): -27.99300 24.39800 x,y,z range (A): 51.56200 54.65700 52.39100 scale (grids/A): 1.954004 object centre (A): 18.69500 54.69450 -1.797501 number of atom coordinates read : 2787 total number of charged atoms : 2676 net assigned charge : 3.162015 assigned positive charge : 427.5065 centred at (gu) : 88.20839 87.16143 92.94205 assigned negative charge : -424.3452 centred at (gu) : 88.07790 86.82581 92.07480 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 84202 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25289 grid for indexing accessible points = 1.400000 m= 32278 mr = 57601 m= 5590 mr = 23872 m= 366 mr = 3529 m= 5 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1097 time to turn everything in is 0.4200000 number of dielectric boundary points 37328 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 162 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 21117 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) : 0.6513347 object centre at (A) : 18.69500 54.69450 -1.797501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.0588863E-03 0.1242562 midg,1,midg; midg,igrid,midg -5.1832076E-02 1.7675104E-02 1,midg,midg; igrid,midg,midg -3.9240297E-02 -9.1651864E-03 gauss-seidel spectral radius is 0.9987288 estimated iterations to convergence 222 setup time was (sec) 0.6400000 now iterating at: 03:44:48 rms-change max change #iterations 4.696125 211.9100 at 10iterations 2.270640 77.30431 at 20iterations 1.093602 35.77009 at 30iterations 0.5268869 17.05361 at 40iterations 0.2534806 7.652592 at 50iterations 0.1222447 3.870140 at 60iterations 5.8758624E-02 1.776308 at 70iterations 2.8299885E-02 0.8119164 at 80iterations 1.3653819E-02 0.3905773 at 90iterations 6.5750466E-03 0.1815777 at 100iterations 3.1704330E-03 9.7944260E-02 at 110iterations 1.5336360E-03 4.5782089E-02 at 120iterations finished qdiffx linear iterations at : 03:44:55 total time elapsed so far: 7.880000 # loops : 120 mean,max change (kT/e) : 1.5336360E-03 4.5782089E-02 energy calculations done at 7.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.010000 DelPhi exited at 03:44:56 8.010u 0.204s 0:08.87 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 Tue Oct 11 2011 at 03:44:56 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 # of charge parameter records: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2787 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.931006 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): -7.086000 44.47600 ymin,ymax (A): 27.36600 82.02299 zmin,zma (A): -27.99300 24.39800 x,y,z range (A): 51.56200 54.65700 52.39100 scale (grids/A): 2.931006 object centre (A): 18.69500 54.69450 -1.797501 number of atom coordinates read : 2787 total number of charged atoms : 2676 net assigned charge : 3.162015 assigned positive charge : 427.5065 centred at (gu) : 87.31248 85.74205 94.41274 assigned negative charge : -424.3452 centred at (gu) : 87.11689 85.23870 93.11214 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 194355 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25289 grid for indexing accessible points = 1.400000 m= 101365 mr = 139679 m= 39436 mr = 82608 m= 10162 mr = 31940 m= 1512 mr = 7581 m= 93 mr = 983 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 3844 time to turn everything in is 1.090000 number of dielectric boundary points 84109 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 21400 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) : 1.954004 object centre at (A) : 18.69500 54.69450 -1.797501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.7754375E-02 1.371296 midg,1,midg; midg,igrid,midg -0.5482844 -8.0004148E-02 1,midg,midg; igrid,midg,midg -0.5768064 -0.2260497 gauss-seidel spectral radius is 0.9992988 estimated iterations to convergence 298 setup time was (sec) 1.320000 now iterating at: 03:44:58 rms-change max change #iterations 11.01041 501.7327 at 10iterations 6.555137 163.3714 at 20iterations 3.889899 87.07155 at 30iterations 2.301076 46.88020 at 40iterations 1.357814 24.77140 at 50iterations 0.8011482 14.35858 at 60iterations 0.4702736 9.006554 at 70iterations 0.2765126 4.922531 at 80iterations 0.1619045 2.895653 at 90iterations 9.4958611E-02 1.763874 at 100iterations 5.5647574E-02 1.066055 at 110iterations 3.2564942E-02 0.5631944 at 120iterations 1.9093081E-02 0.3228264 at 130iterations 1.1162098E-02 0.1911907 at 140iterations 6.5482813E-03 0.1075363 at 150iterations 3.8278943E-03 6.3190460E-02 at 160iterations 2.2501762E-03 3.8795471E-02 at 170iterations 1.3304305E-03 2.3639679E-02 at 180iterations finished qdiffx linear iterations at : 03:45:09 total time elapsed so far: 12.68000 # loops : 180 mean,max change (kT/e) : 1.3304305E-03 2.3639679E-02 energy calculations done at 12.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.81000 DelPhi exited at 03:45:09 12.816u 0.200s 0:13.34 97.5% 0+0k 0+0io 0pf+0w