Mon Oct 10 14:11:44 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 Mon Oct 10 2011 at 14:11:44 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2623 !!! WARNING: HIR 440 has a net charge of 0.5140 !!! WARNING: HIR 444 has a net charge of 0.5140 !!! WARNING: HIR 450 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6219102 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): 16.77400 74.01700 ymin,ymax (A): 12.92000 63.31900 zmin,zma (A): 20.06800 64.70500 x,y,z range (A): 57.24300 50.39900 44.63700 scale (grids/A): 0.6219102 object centre (A): 45.39550 38.11950 42.38650 number of atom coordinates read : 2623 total number of charged atoms : 2483 net assigned charge : -0.9579943 assigned positive charge : 406.9409 centred at (gu) : 90.42190 91.50935 91.43317 assigned negative charge : -407.8994 centred at (gu) : 90.45574 91.30074 91.51128 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6699 nv = 96 ne = 84 npr = 52575 no. pairs analyzed = 52575 no. exposed pairs = 3239 no. arc points = 23627 no. surface atoms = 1090 nbur = 1533 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 362 mr = 3528 m= 2 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 45 time to turn everything in is 0.3100000 number of dielectric boundary points 3487 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2385 ## 236 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8231 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4405723E-09 -9.3002486E-09 midg,1,midg; midg,igrid,midg -1.1915224E-08 1.9752166E-08 1,midg,midg; igrid,midg,midg 1.3882896E-09 -3.7839261E-09 gauss-seidel spectral radius is 0.9866152 estimated iterations to convergence 71 setup time was (sec) 0.5800000 now iterating at: 14:11:46 rms-change max change #iterations 0.1321116 19.14888 at 10iterations 1.2189312E-02 1.762569 at 20iterations 1.1304993E-03 0.1755767 at 30iterations 1.0475190E-04 1.8508911E-02 at 40iterations 9.4726474E-06 1.2741089E-03 at 50iterations finished qdiffx linear iterations at : 14:11:49 total time elapsed so far: 4.410000 # loops : 50 mean,max change (kT/e) : 9.4726474E-06 1.2741089E-03 energy calculations done at 4.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.580000 DelPhi exited at 14:11:50 4.586u 0.372s 0:05.66 87.4% 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 14:11:50 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2623 !!! WARNING: HIR 440 has a net charge of 0.5140 !!! WARNING: HIR 444 has a net charge of 0.5140 !!! WARNING: HIR 450 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.865730 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): 16.77400 74.01700 ymin,ymax (A): 12.92000 63.31900 zmin,zma (A): 20.06800 64.70500 x,y,z range (A): 57.24300 50.39900 44.63700 scale (grids/A): 1.865730 object centre (A): 45.39550 38.11950 42.38650 number of atom coordinates read : 2623 total number of charged atoms : 2483 net assigned charge : -0.9579943 assigned positive charge : 406.9409 centred at (gu) : 91.26507 94.52789 94.29890 assigned negative charge : -407.8994 centred at (gu) : 91.36714 93.90181 94.53328 start vw surface at 0.1100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 72424 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23627 grid for indexing accessible points = 1.400000 m= 23909 mr = 48769 m= 3450 mr = 17037 m= 178 mr = 2042 m= 1 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1402 time to turn everything in is 0.5700000 number of dielectric boundary points 32061 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 164 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 19473 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) : 0.6219102 object centre at (A) : 45.39550 38.11950 42.38650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6265400E-03 -1.4779656E-02 midg,1,midg; midg,igrid,midg -1.7458644E-02 1.4612088E-02 1,midg,midg; igrid,midg,midg 8.6195339E-03 -2.2559211E-02 gauss-seidel spectral radius is 0.9985843 estimated iterations to convergence 211 setup time was (sec) 0.9200000 now iterating at: 14:11:52 rms-change max change #iterations 4.174775 164.5538 at 10iterations 1.926487 71.16810 at 20iterations 0.8850186 29.85901 at 30iterations 0.4060615 14.25139 at 40iterations 0.1883269 6.475479 at 50iterations 8.6791746E-02 2.652963 at 60iterations 4.0035415E-02 1.191793 at 70iterations 1.8473346E-02 0.5924113 at 80iterations 8.5176956E-03 0.3168297 at 90iterations 3.9298506E-03 0.1284370 at 100iterations 1.8088082E-03 6.7197800E-02 at 110iterations 8.3975412E-04 2.7750731E-02 at 120iterations finished qdiffx linear iterations at : 14:12:02 total time elapsed so far: 11.10000 # loops : 120 mean,max change (kT/e) : 8.3975412E-04 2.7750731E-02 energy calculations done at 11.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.26000 DelPhi exited at 14:12:02 11.267u 0.441s 0:12.30 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 14:12:03 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2623 !!! WARNING: HIR 440 has a net charge of 0.5140 !!! WARNING: HIR 444 has a net charge of 0.5140 !!! WARNING: HIR 450 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.798596 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): 16.77400 74.01700 ymin,ymax (A): 12.92000 63.31900 zmin,zma (A): 20.06800 64.70500 x,y,z range (A): 57.24300 50.39900 44.63700 scale (grids/A): 2.798596 object centre (A): 45.39550 38.11950 42.38650 number of atom coordinates read : 2623 total number of charged atoms : 2483 net assigned charge : -0.9579943 assigned positive charge : 406.9409 centred at (gu) : 91.89758 96.79153 96.44822 assigned negative charge : -407.8994 centred at (gu) : 92.05049 95.85265 96.79981 start vw surface at 0.1300000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 168213 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23627 grid for indexing accessible points = 1.400000 m= 78913 mr = 119112 m= 26298 mr = 63474 m= 5927 mr = 20522 m= 811 mr = 4301 m= 42 mr = 523 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 4559 time to turn everything in is 1.490000 number of dielectric boundary points 72269 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 19860 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) : 1.865730 object centre at (A) : 45.39550 38.11950 42.38650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4322975E-02 -0.3049554 midg,1,midg; midg,igrid,midg -0.1511576 0.1400723 1,midg,midg; igrid,midg,midg 0.1814986 -0.1379770 gauss-seidel spectral radius is 0.9992424 estimated iterations to convergence 287 setup time was (sec) 1.820000 now iterating at: 14:12:05 rms-change max change #iterations 9.927381 474.3744 at 10iterations 5.743327 131.2882 at 20iterations 3.301575 65.93509 at 30iterations 1.889138 39.60758 at 40iterations 1.079427 23.24682 at 50iterations 0.6163452 10.98164 at 60iterations 0.3510540 7.243583 at 70iterations 0.2002747 3.580530 at 80iterations 0.1143100 2.053349 at 90iterations 6.5049887E-02 1.183247 at 100iterations 3.6962789E-02 0.6821804 at 110iterations 2.1055344E-02 0.4039946 at 120iterations 1.2056505E-02 0.2246428 at 130iterations 6.8616327E-03 0.1389322 at 140iterations 3.9058360E-03 7.1655273E-02 at 150iterations 2.2230812E-03 4.1822433E-02 at 160iterations 1.2691569E-03 2.3331642E-02 at 170iterations 7.2323496E-04 1.3504028E-02 at 180iterations finished qdiffx linear iterations at : 14:12:21 total time elapsed so far: 18.22000 # loops : 180 mean,max change (kT/e) : 7.2323496E-04 1.3504028E-02 energy calculations done at 18.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.40000 DelPhi exited at 14:12:22 18.403u 0.464s 0:19.44 97.0% 0+0k 0+0io 0pf+0w