Mon Oct 10 10:18:42 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+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 Mon Oct 10 2011 at 10:18:42 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2862 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: 0.5395411 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): -21.83600 44.14600 ymin,ymax (A): 31.84700 86.50900 zmin,zma (A): 26.89100 79.23100 x,y,z range (A): 65.98200 54.66200 52.34000 scale (grids/A): 0.5395411 object centre (A): 11.15500 59.17800 53.06100 number of atom coordinates read : 2862 total number of charged atoms : 2710 net assigned charge : 6.000013 assigned positive charge : 416.4990 centred at (gu) : 91.66892 89.54972 92.97123 assigned negative charge : -410.4993 centred at (gu) : 91.81860 89.50822 93.08037 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5531 nv = 96 ne = 84 npr = 55435 no. pairs analyzed = 55435 no. exposed pairs = 4322 no. arc points = 31540 no. surface atoms = 1437 nbur = 1425 mkacc time = 0.1300000 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 = 1.596000 m= 242 mr = 2384 m= 0 mr = 2 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3101 ## 414 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7261 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9795037E-10 -4.6608817E-10 midg,1,midg; midg,igrid,midg 1.3334885E-10 4.5866005E-10 1,midg,midg; igrid,midg,midg 6.6824779E-10 -6.2854993E-10 gauss-seidel spectral radius is 0.9823015 estimated iterations to convergence 62 setup time was (sec) 0.5600000 now iterating at: 10:18:43 rms-change max change #iterations 6.6880725E-02 13.62309 at 10iterations 4.2916210E-03 0.8004441 at 20iterations 2.9720887E-04 5.7632446E-02 at 30iterations 2.9397701E-05 4.5619011E-03 at 40iterations 4.9449463E-06 6.7615509E-04 at 50iterations finished qdiffx linear iterations at : 10:18:46 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 4.9449463E-06 6.7615509E-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) 3.450000 DelPhi exited at 10:18:46 3.458u 0.146s 0:03.91 91.8% 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 Mon Oct 10 2011 at 10:18:46 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2862 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: 1.618623 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): -21.83600 44.14600 ymin,ymax (A): 31.84700 86.50900 zmin,zma (A): 26.89100 79.23100 x,y,z range (A): 65.98200 54.66200 52.34000 scale (grids/A): 1.618623 object centre (A): 11.15500 59.17800 53.06100 number of atom coordinates read : 2862 total number of charged atoms : 2710 net assigned charge : 6.000013 assigned positive charge : 416.4990 centred at (gu) : 95.00607 88.64867 98.91321 assigned negative charge : -410.4993 centred at (gu) : 95.45551 88.52430 99.24068 start vw surface at 0.1800000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 60216 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31540 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18024 mr = 36404 m= 1899 mr = 11350 m= 60 mr = 717 m= 2 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 31729 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 345 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 20694 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) : 0.5395411 object centre at (A) : 11.15500 59.17800 53.06100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9114305E-03 -7.6991215E-04 midg,1,midg; midg,igrid,midg -2.9780052E-03 1.3404960E-02 1,midg,midg; igrid,midg,midg 1.2669014E-02 -1.3752738E-02 gauss-seidel spectral radius is 0.9981551 estimated iterations to convergence 185 setup time was (sec) 0.7900000 now iterating at: 10:18:47 rms-change max change #iterations 3.094239 182.0034 at 10iterations 1.276300 49.71968 at 20iterations 0.5274234 19.62333 at 30iterations 0.2172382 7.968479 at 40iterations 8.9516230E-02 3.718687 at 50iterations 3.7087269E-02 1.327257 at 60iterations 1.5278914E-02 0.5569801 at 70iterations 6.3140076E-03 0.2506523 at 80iterations 2.6096969E-03 0.1050835 at 90iterations 1.0810774E-03 4.2060852E-02 at 100iterations 4.4879987E-04 1.8123627E-02 at 110iterations 1.8765456E-04 7.1980953E-03 at 120iterations finished qdiffx linear iterations at : 10:18:54 total time elapsed so far: 7.460000 # loops : 120 mean,max change (kT/e) : 1.8765456E-04 7.1980953E-03 energy calculations done at 7.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.660000 DelPhi exited at 10:18:55 7.667u 0.200s 0:08.26 95.1% 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 Mon Oct 10 2011 at 10:18:55 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2862 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.427935 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): -21.83600 44.14600 ymin,ymax (A): 31.84700 86.50900 zmin,zma (A): 26.89100 79.23100 x,y,z range (A): 65.98200 54.66200 52.34000 scale (grids/A): 2.427935 object centre (A): 11.15500 59.17800 53.06100 number of atom coordinates read : 2862 total number of charged atoms : 2710 net assigned charge : 6.000013 assigned positive charge : 416.4990 centred at (gu) : 97.50908 87.97300 103.3697 assigned negative charge : -410.4993 centred at (gu) : 98.18320 87.78630 103.8610 start vw surface at 0.2400000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 139485 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31540 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 61140 mr = 90463 m= 17651 mr = 45371 m= 2698 mr = 12243 m= 155 mr = 1483 m= 10 mr = 44 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 71536 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 21649 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) : 1.618623 object centre at (A) : 11.15500 59.17800 53.06100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4549417E-02 2.1824697E-02 midg,1,midg; midg,igrid,midg -0.1587283 0.2591853 1,midg,midg; igrid,midg,midg 0.3265245 -0.5335600 gauss-seidel spectral radius is 0.9991367 estimated iterations to convergence 269 setup time was (sec) 1.530000 now iterating at: 10:18:56 rms-change max change #iterations 8.317624 281.9462 at 10iterations 4.749424 143.4334 at 20iterations 2.679279 97.14424 at 30iterations 1.507122 40.38166 at 40iterations 0.8400491 23.44011 at 50iterations 0.4674423 11.68133 at 60iterations 0.2588960 6.444477 at 70iterations 0.1432503 3.582230 at 80iterations 7.9043023E-02 1.999182 at 90iterations 4.3655764E-02 1.091427 at 100iterations 2.3994215E-02 0.7036686 at 110iterations 1.3264316E-02 0.2966154 at 120iterations 7.2919093E-03 0.1722555 at 130iterations 3.9989799E-03 8.5353851E-02 at 140iterations 2.1969497E-03 5.3264260E-02 at 150iterations 1.2087487E-03 2.8253555E-02 at 160iterations 6.6424906E-04 1.4300346E-02 at 170iterations 3.6513316E-04 8.9821815E-03 at 180iterations finished qdiffx linear iterations at : 10:19:06 total time elapsed so far: 11.63000 # loops : 180 mean,max change (kT/e) : 3.6513316E-04 8.9821815E-03 energy calculations done at 11.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.82000 DelPhi exited at 10:19:07 11.822u 0.193s 0:12.30 97.6% 0+0k 0+0io 0pf+0w