Sun Oct 9 07:10:30 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 07:10:30 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2011 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 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: 0.7109620 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): -21.88900 24.78300 ymin,ymax (A): -26.23400 23.83900 zmin,zma (A): -13.27900 35.39800 x,y,z range (A): 46.67200 50.07300 48.67700 scale (grids/A): 0.7109620 object centre (A): 1.447001 -1.197499 11.05950 number of atom coordinates read : 2011 total number of charged atoms : 1871 net assigned charge : -0.9999837 assigned positive charge : 304.6589 centred at (gu) : 89.87622 90.09829 89.77666 assigned negative charge : -305.6590 centred at (gu) : 90.02989 90.07571 89.85455 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6879 nv = 96 ne = 84 npr = 42771 no. pairs analyzed = 42771 no. exposed pairs = 2381 no. arc points = 17233 no. surface atoms = 808 nbur = 1203 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 465 mr = 3932 m= 7 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.3100000 number of dielectric boundary points 3337 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1581 ## 128 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7653 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2640028E-08 -4.8278345E-08 midg,1,midg; midg,igrid,midg -2.0767962E-08 2.5584659E-09 1,midg,midg; igrid,midg,midg 7.1775858E-08 -8.8891817E-08 gauss-seidel spectral radius is 0.9896841 estimated iterations to convergence 80 setup time was (sec) 0.5800000 now iterating at: 07:10:31 rms-change max change #iterations 0.2070417 37.31595 at 10iterations 2.5696950E-02 4.141544 at 20iterations 3.1444049E-03 0.4672260 at 30iterations 3.9846820E-04 6.0621023E-02 at 40iterations 4.9178489E-05 6.7596436E-03 at 50iterations finished qdiffx linear iterations at : 07:10:34 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 4.9178489E-05 6.7596436E-03 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.030000 DelPhi exited at 07:10:35 4.032u 0.243s 0:04.58 93.2% 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 07:10:35 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2011 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 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: 2.132886 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): -21.88900 24.78300 ymin,ymax (A): -26.23400 23.83900 zmin,zma (A): -13.27900 35.39800 x,y,z range (A): 46.67200 50.07300 48.67700 scale (grids/A): 2.132886 object centre (A): 1.447001 -1.197499 11.05950 number of atom coordinates read : 2011 total number of charged atoms : 1871 net assigned charge : -0.9999837 assigned positive charge : 304.6589 centred at (gu) : 89.62842 90.29459 89.32975 assigned negative charge : -305.6590 centred at (gu) : 90.08965 90.22712 89.56356 start vw surface at 0.1400000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 72914 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17233 grid for indexing accessible points = 1.400000 m= 28426 mr = 50837 m= 5778 mr = 21890 m= 497 mr = 4003 m= 14 mr = 267 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 765 time to turn everything in is 0.6600000 number of dielectric boundary points 30632 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 61 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 14870 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) : 0.7109620 object centre at (A) : 1.447001 -1.197499 11.05950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.9804193E-03 -6.3536718E-02 midg,1,midg; midg,igrid,midg 1.6734960E-02 -3.0578209E-02 1,midg,midg; igrid,midg,midg 4.3786559E-02 -1.1399703E-02 gauss-seidel spectral radius is 0.9988402 estimated iterations to convergence 232 setup time was (sec) 0.9500000 now iterating at: 07:10:36 rms-change max change #iterations 4.717360 250.4043 at 10iterations 2.325197 84.53171 at 20iterations 1.157944 35.81987 at 30iterations 0.5761125 18.02612 at 40iterations 0.2850175 10.44598 at 50iterations 0.1416804 4.180688 at 60iterations 7.0363849E-02 1.974645 at 70iterations 3.5024088E-02 1.026531 at 80iterations 1.7436521E-02 0.5745193 at 90iterations 8.6842170E-03 0.2790701 at 100iterations 4.3047341E-03 0.1278553 at 110iterations 2.1450946E-03 6.2408447E-02 at 120iterations finished qdiffx linear iterations at : 07:10:44 total time elapsed so far: 9.210000 # loops : 120 mean,max change (kT/e) : 2.1450946E-03 6.2408447E-02 energy calculations done at 9.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.390000 DelPhi exited at 07:10:45 9.390u 0.294s 0:09.97 97.0% 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 07:10:45 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2011 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 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: 3.199329 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): -21.88900 24.78300 ymin,ymax (A): -26.23400 23.83900 zmin,zma (A): -13.27900 35.39800 x,y,z range (A): 46.67200 50.07300 48.67700 scale (grids/A): 3.199329 object centre (A): 1.447001 -1.197499 11.05950 number of atom coordinates read : 2011 total number of charged atoms : 1871 net assigned charge : -0.9999837 assigned positive charge : 304.6589 centred at (gu) : 89.44260 90.44198 88.99460 assigned negative charge : -305.6590 centred at (gu) : 90.13453 90.34062 89.34536 start vw surface at 0.1600000 fill in re-entrant regions at 0.9900000 boundary points on vw surface= 168160 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17233 grid for indexing accessible points = 1.400000 m= 88555 mr = 122397 m= 36516 mr = 74056 m= 10990 mr = 30503 m= 2162 mr = 8829 m= 224 mr = 1600 m= 8 mr = 135 m= 0 mr = 5 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 2321 time to turn everything in is 2.160000 number of dielectric boundary points 69090 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.310000 number of grid points assigned charge 14968 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) : 2.132886 object centre at (A) : 1.447001 -1.197499 11.05950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.8885797E-02 -0.6654247 midg,1,midg; midg,igrid,midg 0.2894107 -0.3807628 1,midg,midg; igrid,midg,midg 0.2934336 -0.1105045 gauss-seidel spectral radius is 0.9993002 estimated iterations to convergence 298 setup time was (sec) 2.490000 now iterating at: 07:10:48 rms-change max change #iterations 10.33298 458.3219 at 10iterations 5.999649 135.8580 at 20iterations 3.495901 59.77336 at 30iterations 2.037220 36.72080 at 40iterations 1.191290 21.89612 at 50iterations 0.6931386 13.41569 at 60iterations 0.4023170 8.022286 at 70iterations 0.2345134 4.121803 at 80iterations 0.1368974 2.387400 at 90iterations 7.9779901E-02 1.469456 at 100iterations 4.6405125E-02 0.7841352 at 110iterations 2.7039167E-02 0.4654169 at 120iterations 1.5767649E-02 0.2503967 at 130iterations 9.1740889E-03 0.1570239 at 140iterations 5.3456561E-03 0.1000667 at 150iterations 3.1227036E-03 5.3142548E-02 at 160iterations 1.8170868E-03 3.2591611E-02 at 170iterations 1.0572275E-03 1.8357277E-02 at 180iterations finished qdiffx linear iterations at : 07:11:01 total time elapsed so far: 16.24000 # loops : 180 mean,max change (kT/e) : 1.0572275E-03 1.8357277E-02 energy calculations done at 16.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.42000 DelPhi exited at 07:11:02 16.418u 0.288s 0:16.96 98.4% 0+0k 0+0io 0pf+0w