Sat Oct 15 12:29:31 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 15 2011 at 12:29:31 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2058 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -6.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6986694 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): -23.01000 24.92700 ymin,ymax (A): -25.48000 23.59300 zmin,zma (A): -14.55400 36.40000 x,y,z range (A): 47.93700 49.07300 50.95400 scale (grids/A): 0.6986694 object centre (A): 0.9584999 -0.9434996 10.92300 number of atom coordinates read : 2058 total number of charged atoms : 1919 net assigned charge : -3.999983 assigned positive charge : 314.8539 centred at (gu) : 90.19804 89.65579 90.11675 assigned negative charge : -318.8540 centred at (gu) : 90.31948 89.58392 90.23543 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6640 nv = 96 ne = 84 npr = 45540 no. pairs analyzed = 45540 no. exposed pairs = 2495 no. arc points = 17869 no. surface atoms = 837 nbur = 1221 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 378 mr = 3660 m= 3 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 48 time to turn everything in is 0.1700000 number of dielectric boundary points 3295 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1631 ## 147 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7480 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1085436E-08 -7.8588712E-08 midg,1,midg; midg,igrid,midg -6.1005110E-08 2.3110753E-09 1,midg,midg; igrid,midg,midg 2.1791914E-08 -8.1087656E-08 gauss-seidel spectral radius is 0.9893234 estimated iterations to convergence 79 setup time was (sec) 0.3600000 now iterating at: 12:29:31 rms-change max change #iterations 0.2097539 32.99933 at 10iterations 2.5064839E-02 3.325441 at 20iterations 3.0024315E-03 0.4470065 at 30iterations 3.6206155E-04 4.6850204E-02 at 40iterations 4.3063803E-05 5.9738159E-03 at 50iterations finished qdiffx linear iterations at : 12:29:34 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 4.3063803E-05 5.9738159E-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) 3.350000 DelPhi exited at 12:29:35 3.356u 0.171s 0:03.87 90.9% 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 Sat Oct 15 2011 at 12:29:35 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2058 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -6.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.096008 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): -23.01000 24.92700 ymin,ymax (A): -25.48000 23.59300 zmin,zma (A): -14.55400 36.40000 x,y,z range (A): 47.93700 49.07300 50.95400 scale (grids/A): 2.096008 object centre (A): 0.9584999 -0.9434996 10.92300 number of atom coordinates read : 2058 total number of charged atoms : 1919 net assigned charge : -3.999983 assigned positive charge : 314.8539 centred at (gu) : 90.59420 88.96735 90.35030 assigned negative charge : -318.8540 centred at (gu) : 90.95838 88.75165 90.70621 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70086 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17869 grid for indexing accessible points = 1.400000 m= 26489 mr = 48011 m= 4991 mr = 20024 m= 446 mr = 3336 m= 13 mr = 265 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1217 time to turn everything in is 0.3500000 number of dielectric boundary points 30389 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 90 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 15160 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) : 0.6986694 object centre at (A) : 0.9584999 -0.9434996 10.92300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0295123E-03 -7.9909354E-02 midg,1,midg; midg,igrid,midg -9.7967656E-03 -2.5823314E-02 1,midg,midg; igrid,midg,midg 3.3019181E-02 1.0018249E-03 gauss-seidel spectral radius is 0.9988064 estimated iterations to convergence 229 setup time was (sec) 0.5700000 now iterating at: 12:29:35 rms-change max change #iterations 4.756866 223.9000 at 10iterations 2.328969 93.69875 at 20iterations 1.142643 56.45587 at 30iterations 0.5631296 20.03681 at 40iterations 0.2776646 8.982942 at 50iterations 0.1363525 4.172638 at 60iterations 6.7083538E-02 2.151207 at 70iterations 3.2962244E-02 1.077626 at 80iterations 1.6180081E-02 0.4933987 at 90iterations 7.9732332E-03 0.2426748 at 100iterations 3.9106314E-03 0.1167085 at 110iterations 1.9314016E-03 6.3446045E-02 at 120iterations finished qdiffx linear iterations at : 12:29:42 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 1.9314016E-03 6.3446045E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 12:29:43 7.768u 0.204s 0:08.24 96.6% 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 15 2011 at 12:29:43 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2058 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -6.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.144012 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): -23.01000 24.92700 ymin,ymax (A): -25.48000 23.59300 zmin,zma (A): -14.55400 36.40000 x,y,z range (A): 47.93700 49.07300 50.95400 scale (grids/A): 3.144012 object centre (A): 0.9584999 -0.9434996 10.92300 number of atom coordinates read : 2058 total number of charged atoms : 1919 net assigned charge : -3.999983 assigned positive charge : 314.8539 centred at (gu) : 90.89130 88.45089 90.52543 assigned negative charge : -318.8540 centred at (gu) : 91.43754 88.12746 91.05931 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 161752 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17869 grid for indexing accessible points = 1.400000 m= 82982 mr = 115989 m= 33142 mr = 68640 m= 9428 mr = 27317 m= 1849 mr = 7367 m= 256 mr = 1408 m= 16 mr = 182 m= 0 mr = 7 time to grow re-entrant surface = 0.5199999 no. cavity mid-points inaccessible to solvent = 4274 time to turn everything in is 1.080000 number of dielectric boundary points 68515 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 15322 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) : 2.096008 object centre at (A) : 0.9584999 -0.9434996 10.92300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1890006 -0.8232214 midg,1,midg; midg,igrid,midg 6.1472703E-02 -0.3056130 1,midg,midg; igrid,midg,midg 0.2275345 -1.6080394E-02 gauss-seidel spectral radius is 0.9992927 estimated iterations to convergence 297 setup time was (sec) 1.310000 now iterating at: 12:29:44 rms-change max change #iterations 10.63412 425.6559 at 10iterations 6.149017 164.1733 at 20iterations 3.574480 84.92974 at 30iterations 2.075182 54.87503 at 40iterations 1.208279 22.44784 at 50iterations 0.7020144 13.68973 at 60iterations 0.4070093 7.971448 at 70iterations 0.2362739 4.168266 at 80iterations 0.1372381 2.519180 at 90iterations 7.9656869E-02 1.336124 at 100iterations 4.6233445E-02 0.8059039 at 110iterations 2.6880195E-02 0.4513226 at 120iterations 1.5582846E-02 0.2674637 at 130iterations 9.0589821E-03 0.1551379 at 140iterations 5.2415244E-03 8.9863896E-02 at 150iterations 3.0558412E-03 5.8588028E-02 at 160iterations 1.7725133E-03 3.0916214E-02 at 170iterations 1.0284757E-03 1.9210815E-02 at 180iterations finished qdiffx linear iterations at : 12:29:56 total time elapsed so far: 12.62000 # loops : 180 mean,max change (kT/e) : 1.0284757E-03 1.9210815E-02 energy calculations done at 12.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.75000 DelPhi exited at 12:29:56 12.756u 0.211s 0:13.24 97.8% 0+0k 0+0io 0pf+0w