Wed Dec 28 11:03:25 PST 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 Wed Dec 28 2011 at 11:03:25 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1967 !!! WARNING: ASH 124 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6064426 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): -24.01900 34.68400 ymin,ymax (A): -20.31200 20.66600 zmin,zma (A): -2.784000 39.31000 x,y,z range (A): 58.70300 40.97800 42.09400 scale (grids/A): 0.6064426 object centre (A): 5.332501 0.1770000 18.26300 number of atom coordinates read : 1967 total number of charged atoms : 1834 net assigned charge : 4.681011 assigned positive charge : 292.5899 centred at (gu) : 89.82979 90.62377 90.21972 assigned negative charge : -287.9093 centred at (gu) : 89.84386 90.72562 90.36290 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 4891 nv = 96 ne = 84 npr = 40139 no. pairs analyzed = 40139 no. exposed pairs = 2528 no. arc points = 17681 no. surface atoms = 855 nbur = 1112 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 217 mr = 2610 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 2482 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1801 ## 183 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 5900 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.8093011E-09 -2.4178477E-09 midg,1,midg; midg,igrid,midg 5.0709508E-09 -1.0493704E-09 1,midg,midg; igrid,midg,midg 3.0845035E-09 1.9701163E-09 gauss-seidel spectral radius is 0.9858714 estimated iterations to convergence 69 setup time was (sec) 0.5900000 now iterating at: 11:03:26 rms-change max change #iterations 0.1001263 18.87291 at 10iterations 8.7148640E-03 1.472000 at 20iterations 7.4641034E-04 0.1257095 at 30iterations 6.5430635E-05 1.1400223E-02 at 40iterations 5.5677556E-06 1.1024475E-03 at 50iterations finished qdiffx linear iterations at : 11:03:30 total time elapsed so far: 4.360000 # loops : 50 mean,max change (kT/e) : 5.5677556E-06 1.1024475E-03 energy calculations done at 4.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.630000 DelPhi exited at 11:03:30 4.629u 0.215s 0:05.30 91.1% 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 Dec 28 2011 at 11:03:31 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1967 !!! WARNING: ASH 124 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.819328 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): -24.01900 34.68400 ymin,ymax (A): -20.31200 20.66600 zmin,zma (A): -2.784000 39.31000 x,y,z range (A): 58.70300 40.97800 42.09400 scale (grids/A): 1.819328 object centre (A): 5.332501 0.1770000 18.26300 number of atom coordinates read : 1967 total number of charged atoms : 1834 net assigned charge : 4.681011 assigned positive charge : 292.5899 centred at (gu) : 89.48945 91.87139 90.65920 assigned negative charge : -287.9093 centred at (gu) : 89.53175 92.17709 91.08901 start vw surface at 0.2100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 52751 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17681 grid for indexing accessible points = 1.400000 m= 18694 mr = 35818 m= 2620 mr = 13965 m= 107 mr = 1561 m= 0 mr = 18 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 581 time to turn everything in is 0.5900000 number of dielectric boundary points 22810 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 136 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 14331 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) : 0.6064426 object centre at (A) : 5.332501 0.1770000 18.26300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0790349E-02 -2.8058561E-03 midg,1,midg; midg,igrid,midg 9.3701305E-03 1.1822092E-03 1,midg,midg; igrid,midg,midg 2.9928077E-02 2.1339368E-02 gauss-seidel spectral radius is 0.9984303 estimated iterations to convergence 200 setup time was (sec) 0.9300000 now iterating at: 11:03:32 rms-change max change #iterations 3.327786 187.3357 at 10iterations 1.470896 63.42931 at 20iterations 0.6522730 24.91972 at 30iterations 0.2890213 10.26227 at 40iterations 0.1279136 5.117720 at 50iterations 5.6719966E-02 2.128147 at 60iterations 2.5122536E-02 0.9367962 at 70iterations 1.1131075E-02 0.4318314 at 80iterations 4.9181716E-03 0.1956444 at 90iterations 2.1803894E-03 7.9941273E-02 at 100iterations 9.6827198E-04 3.9912701E-02 at 110iterations 4.2904521E-04 1.5932083E-02 at 120iterations finished qdiffx linear iterations at : 11:03:40 total time elapsed so far: 9.050000 # loops : 120 mean,max change (kT/e) : 4.2904521E-04 1.5932083E-02 energy calculations done at 9.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.290000 DelPhi exited at 11:03:40 9.288u 0.250s 0:09.94 95.8% 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 Wed Dec 28 2011 at 11:03:42 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1967 !!! WARNING: ASH 124 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.728992 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): -24.01900 34.68400 ymin,ymax (A): -20.31200 20.66600 zmin,zma (A): -2.784000 39.31000 x,y,z range (A): 58.70300 40.97800 42.09400 scale (grids/A): 2.728992 object centre (A): 5.332501 0.1770000 18.26300 number of atom coordinates read : 1967 total number of charged atoms : 1834 net assigned charge : 4.681011 assigned positive charge : 292.5899 centred at (gu) : 89.23421 92.80709 90.98883 assigned negative charge : -287.9093 centred at (gu) : 89.29771 93.26561 91.63351 start vw surface at 0.2000000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 121621 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17681 grid for indexing accessible points = 1.400000 m= 61168 mr = 86740 m= 21443 mr = 50130 m= 4444 mr = 17379 m= 464 mr = 3296 m= 19 mr = 286 m= 0 mr = 2 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 1989 time to turn everything in is 1.280000 number of dielectric boundary points 51326 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 14669 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) : 1.819328 object centre at (A) : 5.332501 0.1770000 18.26300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.1523446E-02 -1.0843464E-02 midg,1,midg; midg,igrid,midg 8.2528025E-02 4.3702014E-02 1,midg,midg; igrid,midg,midg 0.3024363 0.2073905 gauss-seidel spectral radius is 0.9991839 estimated iterations to convergence 276 setup time was (sec) 1.630000 now iterating at: 11:03:43 rms-change max change #iterations 7.998982 318.4009 at 10iterations 4.543315 124.5343 at 20iterations 2.555749 71.23320 at 30iterations 1.435967 32.30988 at 40iterations 0.8064225 20.35107 at 50iterations 0.4496276 9.595070 at 60iterations 0.2509336 5.507436 at 70iterations 0.1403206 3.012182 at 80iterations 7.8482956E-02 1.913673 at 90iterations 4.3794192E-02 1.018167 at 100iterations 2.4405053E-02 0.5523593 at 110iterations 1.3648398E-02 0.3232384 at 120iterations 7.5956318E-03 0.1672421 at 130iterations 4.2383145E-03 9.4615936E-02 at 140iterations 2.3677784E-03 4.8830032E-02 at 150iterations 1.3199402E-03 2.9117584E-02 at 160iterations 7.3549611E-04 1.6448975E-02 at 170iterations 4.1004003E-04 8.5868835E-03 at 180iterations finished qdiffx linear iterations at : 11:03:56 total time elapsed so far: 14.20000 # loops : 180 mean,max change (kT/e) : 4.1004003E-04 8.5868835E-03 energy calculations done at 14.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.44000 DelPhi exited at 11:03:57 14.437u 0.211s 0:15.19 96.3% 0+0k 0+0io 0pf+0w