Mon Oct 10 17:04:26 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 17:04:26 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2791 !!! WARNING: HIZ 617 has a net charge of 0.2000 !!! WARNING: HIZ 653 has a net charge of 0.2000 !!! WARNING: GLU 858 has a net charge of -2.0000 !!! WARNING: MG8 866 has a net charge of 1.4000 !!! WARNING: ZN8 867 has a net charge of 1.4000 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: 0.5828326 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): -14.99700 46.08400 ymin,ymax (A): -30.80600 26.72500 zmin,zma (A): -7.461000 41.24400 x,y,z range (A): 61.08100 57.53100 48.70500 scale (grids/A): 0.5828326 object centre (A): 15.54350 -2.040500 16.89150 number of atom coordinates read : 2791 total number of charged atoms : 2647 net assigned charge : -0.2999849 assigned positive charge : 420.0094 centred at (gu) : 88.02097 90.25876 90.75826 assigned negative charge : -420.3104 centred at (gu) : 88.12739 90.19564 90.75987 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6095 nv = 96 ne = 84 npr = 57770 no. pairs analyzed = 57770 no. exposed pairs = 3428 no. arc points = 23790 no. surface atoms = 1157 nbur = 1634 mkacc time = 0.1500000 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 = 1.484000 m= 242 mr = 3226 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3096 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2459 ## 274 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7809 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.6752757E-11 -1.9656295E-10 midg,1,midg; midg,igrid,midg -1.4813143E-09 1.3800162E-09 1,midg,midg; igrid,midg,midg 3.6430703E-09 -1.6225826E-09 gauss-seidel spectral radius is 0.9847864 estimated iterations to convergence 67 setup time was (sec) 0.6600000 now iterating at: 17:04:27 rms-change max change #iterations 9.6319877E-02 14.43301 at 10iterations 7.6088989E-03 1.303860 at 20iterations 6.8058772E-04 0.1047373 at 30iterations 8.0067468E-05 1.4968872E-02 at 40iterations 1.5198065E-05 2.5501251E-03 at 50iterations finished qdiffx linear iterations at : 17:04:32 total time elapsed so far: 4.970000 # loops : 50 mean,max change (kT/e) : 1.5198065E-05 2.5501251E-03 energy calculations done at 4.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.150000 DelPhi exited at 17:04:33 5.150u 0.432s 0:06.43 86.7% 0+0k 0+0io 6pf+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 17:04:33 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2791 !!! WARNING: HIZ 617 has a net charge of 0.2000 !!! WARNING: HIZ 653 has a net charge of 0.2000 !!! WARNING: GLU 858 has a net charge of -2.0000 !!! WARNING: MG8 866 has a net charge of 1.4000 !!! WARNING: ZN8 867 has a net charge of 1.4000 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: 1.748498 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): -14.99700 46.08400 ymin,ymax (A): -30.80600 26.72500 zmin,zma (A): -7.461000 41.24400 x,y,z range (A): 61.08100 57.53100 48.70500 scale (grids/A): 1.748498 object centre (A): 15.54350 -2.040500 16.89150 number of atom coordinates read : 2791 total number of charged atoms : 2647 net assigned charge : -0.2999849 assigned positive charge : 420.0094 centred at (gu) : 84.06220 90.77565 92.27386 assigned negative charge : -420.3104 centred at (gu) : 84.38194 90.58649 92.27927 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 67546 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23790 grid for indexing accessible points = 1.400000 m= 21697 mr = 46409 m= 2676 mr = 15302 m= 89 mr = 1523 m= 0 mr = 13 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 182 time to turn everything in is 0.5600000 number of dielectric boundary points 28761 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 229 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 20559 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) : 0.5828326 object centre at (A) : 15.54350 -2.040500 16.89150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6090127E-03 3.9162431E-03 midg,1,midg; midg,igrid,midg -3.1086833E-03 9.3443450E-03 1,midg,midg; igrid,midg,midg 2.3350596E-02 -1.0590506E-02 gauss-seidel spectral radius is 0.9984007 estimated iterations to convergence 198 setup time was (sec) 0.9300000 now iterating at: 17:04:35 rms-change max change #iterations 3.747531 147.4234 at 10iterations 1.652733 57.07490 at 20iterations 0.7265357 27.66369 at 30iterations 0.3209028 11.15919 at 40iterations 0.1413368 5.124292 at 50iterations 6.2438820E-02 2.179708 at 60iterations 2.7378708E-02 0.9086829 at 70iterations 1.2099333E-02 0.4647981 at 80iterations 5.3426451E-03 0.2045193 at 90iterations 2.3553765E-03 7.5757980E-02 at 100iterations 1.0384171E-03 3.6204159E-02 at 110iterations 4.5942230E-04 1.5953064E-02 at 120iterations finished qdiffx linear iterations at : 17:04:45 total time elapsed so far: 11.54000 # loops : 120 mean,max change (kT/e) : 4.5942230E-04 1.5953064E-02 energy calculations done at 11.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.72000 DelPhi exited at 17:04:46 11.724u 0.514s 0:12.86 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 17:04:46 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2791 !!! WARNING: HIZ 617 has a net charge of 0.2000 !!! WARNING: HIZ 653 has a net charge of 0.2000 !!! WARNING: GLU 858 has a net charge of -2.0000 !!! WARNING: MG8 866 has a net charge of 1.4000 !!! WARNING: ZN8 867 has a net charge of 1.4000 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: 2.622747 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): -14.99700 46.08400 ymin,ymax (A): -30.80600 26.72500 zmin,zma (A): -7.461000 41.24400 x,y,z range (A): 61.08100 57.53100 48.70500 scale (grids/A): 2.622747 object centre (A): 15.54350 -2.040500 16.89150 number of atom coordinates read : 2791 total number of charged atoms : 2647 net assigned charge : -0.2999849 assigned positive charge : 420.0094 centred at (gu) : 81.09310 91.16313 93.41052 assigned negative charge : -420.3104 centred at (gu) : 81.57280 90.87964 93.41881 start vw surface at 0.1200000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 157227 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23790 grid for indexing accessible points = 1.400000 m= 72921 mr = 113722 m= 23192 mr = 58154 m= 4456 mr = 17906 m= 390 mr = 3259 m= 10 mr = 232 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 564 time to turn everything in is 1.420000 number of dielectric boundary points 64923 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 21164 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) : 1.748498 object centre at (A) : 15.54350 -2.040500 16.89150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2133426E-02 9.1951571E-02 midg,1,midg; midg,igrid,midg 1.0543030E-03 0.1495126 1,midg,midg; igrid,midg,midg 0.6085041 -0.1573173 gauss-seidel spectral radius is 0.9991989 estimated iterations to convergence 279 setup time was (sec) 1.800000 now iterating at: 17:04:48 rms-change max change #iterations 9.209110 275.4871 at 10iterations 5.258701 118.0792 at 20iterations 2.983716 82.14487 at 30iterations 1.694269 42.07910 at 40iterations 0.9579412 21.69025 at 50iterations 0.5396898 10.78125 at 60iterations 0.3049426 6.333811 at 70iterations 0.1712394 3.498808 at 80iterations 9.6580297E-02 1.928602 at 90iterations 5.4229513E-02 1.016556 at 100iterations 3.0495083E-02 0.5992050 at 110iterations 1.7138163E-02 0.3383379 at 120iterations 9.6467584E-03 0.1790862 at 130iterations 5.4282174E-03 0.1027207 at 140iterations 3.0458479E-03 5.7025909E-02 at 150iterations 1.7154274E-03 3.8222402E-02 at 160iterations 9.6680981E-04 1.9023895E-02 at 170iterations 5.4644933E-04 1.0963440E-02 at 180iterations finished qdiffx linear iterations at : 17:05:06 total time elapsed so far: 19.36000 # loops : 180 mean,max change (kT/e) : 5.4644933E-04 1.0963440E-02 energy calculations done at 19.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.52000 DelPhi exited at 17:05:07 19.521u 0.545s 0:20.55 97.6% 0+0k 0+0io 0pf+0w