Sun Oct 9 14:15:42 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 14:15:42 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2659 !!! WARNING: HIR 183 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5665632 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): -1.184000 51.53000 ymin,ymax (A): -7.916000 39.40400 zmin,zma (A): -15.14700 47.68800 x,y,z range (A): 52.71400 47.32000 62.83500 scale (grids/A): 0.5665632 object centre (A): 25.17300 15.74400 16.27050 number of atom coordinates read : 2659 total number of charged atoms : 2520 net assigned charge : 8.014018 assigned positive charge : 403.4305 centred at (gu) : 89.53552 90.24699 89.09866 assigned negative charge : -395.4175 centred at (gu) : 89.53652 90.13892 89.12676 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5573 nv = 96 ne = 84 npr = 52649 no. pairs analyzed = 52649 no. exposed pairs = 3433 no. arc points = 24078 no. surface atoms = 1148 nbur = 1511 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 242 mr = 2810 m= 0 mr = 11 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 2994 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2432 ## 317 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7131 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7635282E-09 5.9462191E-10 midg,1,midg; midg,igrid,midg -2.6128313E-10 2.5475113E-09 1,midg,midg; igrid,midg,midg 1.2149750E-09 9.5736896E-10 gauss-seidel spectral radius is 0.9839028 estimated iterations to convergence 65 setup time was (sec) 0.3500000 now iterating at: 14:15:43 rms-change max change #iterations 8.5116521E-02 17.86310 at 10iterations 6.1400314E-03 0.9028435 at 20iterations 4.5673421E-04 9.0671539E-02 at 30iterations 3.6259775E-05 6.2446594E-03 at 40iterations 3.7076711E-06 6.0272217E-04 at 50iterations finished qdiffx linear iterations at : 14:15:46 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 3.7076711E-06 6.0272217E-04 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 14:15:46 3.379u 0.212s 0:03.86 92.7% 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 14:15:46 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2659 !!! WARNING: HIR 183 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.699690 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): -1.184000 51.53000 ymin,ymax (A): -7.916000 39.40400 zmin,zma (A): -15.14700 47.68800 x,y,z range (A): 52.71400 47.32000 62.83500 scale (grids/A): 1.699690 object centre (A): 25.17300 15.74400 16.27050 number of atom coordinates read : 2659 total number of charged atoms : 2520 net assigned charge : 8.014018 assigned positive charge : 403.4305 centred at (gu) : 88.60596 90.74025 87.29547 assigned negative charge : -395.4175 centred at (gu) : 88.60929 90.41664 87.37986 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 61885 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24078 grid for indexing accessible points = 1.400000 m= 19061 mr = 41617 m= 1969 mr = 12687 m= 73 mr = 860 m= 1 mr = 8 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 0.3200000 number of dielectric boundary points 27817 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 304 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 19433 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) : 0.5665632 object centre at (A) : 25.17300 15.74400 16.27050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3266311E-02 1.2247275E-02 midg,1,midg; midg,igrid,midg -8.4295898E-04 4.8020952E-03 1,midg,midg; igrid,midg,midg 2.7355447E-03 5.8455616E-03 gauss-seidel spectral radius is 0.9983041 estimated iterations to convergence 193 setup time was (sec) 0.5200000 now iterating at: 14:15:47 rms-change max change #iterations 3.398354 170.4338 at 10iterations 1.452582 58.33234 at 20iterations 0.6245201 23.35798 at 30iterations 0.2685292 10.26675 at 40iterations 0.1149275 4.250181 at 50iterations 4.9113985E-02 2.015186 at 60iterations 2.1186840E-02 0.7373257 at 70iterations 9.0779085E-03 0.3548412 at 80iterations 3.8975368E-03 0.1476479 at 90iterations 1.6729299E-03 6.2363625E-02 at 100iterations 7.2018855E-04 2.5809288E-02 at 110iterations 3.1101544E-04 1.1730194E-02 at 120iterations finished qdiffx linear iterations at : 14:15:54 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 3.1101544E-04 1.1730194E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 14:15:54 7.736u 0.206s 0:08.23 96.3% 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 14:15:55 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2659 !!! WARNING: HIR 183 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.549535 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): -1.184000 51.53000 ymin,ymax (A): -7.916000 39.40400 zmin,zma (A): -15.14700 47.68800 x,y,z range (A): 52.71400 47.32000 62.83500 scale (grids/A): 2.549535 object centre (A): 25.17300 15.74400 16.27050 number of atom coordinates read : 2659 total number of charged atoms : 2520 net assigned charge : 8.014018 assigned positive charge : 403.4305 centred at (gu) : 87.90867 91.11031 85.94305 assigned negative charge : -395.4175 centred at (gu) : 87.91366 90.62479 86.06979 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 143373 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24078 grid for indexing accessible points = 1.400000 m= 65786 mr = 101735 m= 18763 mr = 51270 m= 3091 mr = 13558 m= 298 mr = 1852 m= 9 mr = 151 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7600000 number of dielectric boundary points 62754 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 20145 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) : 1.699690 object centre at (A) : 25.17300 15.74400 16.27050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5847130 0.2035493 midg,1,midg; midg,igrid,midg -1.2511651E-02 8.3866902E-03 1,midg,midg; igrid,midg,midg 3.9393127E-02 4.6800710E-02 gauss-seidel spectral radius is 0.9991690 estimated iterations to convergence 274 setup time was (sec) 1.000000 now iterating at: 14:15:56 rms-change max change #iterations 8.673127 308.0212 at 10iterations 4.968357 149.5033 at 20iterations 2.835031 79.71090 at 30iterations 1.599308 37.17995 at 40iterations 0.9030992 19.37558 at 50iterations 0.5060102 11.00337 at 60iterations 0.2840505 6.828358 at 70iterations 0.1588035 3.529167 at 80iterations 8.8871278E-02 2.006577 at 90iterations 4.9522206E-02 1.069381 at 100iterations 2.7627818E-02 0.5759220 at 110iterations 1.5378706E-02 0.3257732 at 120iterations 8.5788639E-03 0.1946526 at 130iterations 4.7712261E-03 9.7574234E-02 at 140iterations 2.6557411E-03 5.8286667E-02 at 150iterations 1.4749561E-03 2.9846191E-02 at 160iterations 8.2351937E-04 2.0580292E-02 at 170iterations 4.5796437E-04 9.8457336E-03 at 180iterations finished qdiffx linear iterations at : 14:16:07 total time elapsed so far: 12.19000 # loops : 180 mean,max change (kT/e) : 4.5796437E-04 9.8457336E-03 energy calculations done at 12.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.28000 DelPhi exited at 14:16:07 12.278u 0.246s 0:12.83 97.5% 0+0k 0+0io 0pf+0w