Tue Nov 22 14:19:02 PST 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 Tue Nov 22 2011 at 14:19:07 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5907929 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): -35.28200 10.11700 ymin,ymax (A): 1.296000 41.66000 zmin,zma (A): -1.630000 58.62800 x,y,z range (A): 45.39900 40.36400 60.25800 scale (grids/A): 0.5907929 object centre (A): -12.58250 21.47800 28.49900 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.0260 centred at (gu) : 90.37815 89.43269 89.55544 assigned negative charge : -288.0262 centred at (gu) : 90.32622 89.57146 89.54211 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4636 nv = 96 ne = 84 npr = 40115 no. pairs analyzed = 40115 no. exposed pairs = 2433 no. arc points = 16894 no. surface atoms = 831 nbur = 1133 mkacc time = 7.0000000E-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 = 1.484000 m= 198 mr = 2501 m= 0 mr = 22 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1500000 number of dielectric boundary points 2311 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1725 ## 197 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 5639 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.2539852E-10 1.0852168E-09 midg,1,midg; midg,igrid,midg 4.2180455E-09 -1.6850736E-09 1,midg,midg; igrid,midg,midg -1.1528223E-10 2.1547615E-09 gauss-seidel spectral radius is 0.9851228 estimated iterations to convergence 67 setup time was (sec) 0.3700000 now iterating at: 14:19:11 rms-change max change #iterations 8.6918145E-02 15.04252 at 10iterations 7.0630694E-03 1.214005 at 20iterations 5.6812778E-04 9.8915100E-02 at 30iterations 4.6488549E-05 7.9383850E-03 at 40iterations 3.8026751E-06 6.2847137E-04 at 50iterations finished qdiffx linear iterations at : 14:19:21 total time elapsed so far: 3.760000 # loops : 50 mean,max change (kT/e) : 3.8026751E-06 6.2847137E-04 energy calculations done at 3.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.900000 DelPhi exited at 14:19:22 3.903u 0.249s 0:15.71 26.3% 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 Tue Nov 22 2011 at 14:19:25 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.772379 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): -35.28200 10.11700 ymin,ymax (A): 1.296000 41.66000 zmin,zma (A): -1.630000 58.62800 x,y,z range (A): 45.39900 40.36400 60.25800 scale (grids/A): 1.772379 object centre (A): -12.58250 21.47800 28.49900 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.0260 centred at (gu) : 91.13418 88.29797 88.66627 assigned negative charge : -288.0262 centred at (gu) : 90.97876 88.71456 88.62650 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 49994 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16894 grid for indexing accessible points = 1.400000 m= 17783 mr = 34258 m= 2402 mr = 13347 m= 111 mr = 1487 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 338 time to turn everything in is 0.2600000 number of dielectric boundary points 21176 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 155 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 14278 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) : 0.5907929 object centre at (A) : -12.58250 21.47800 28.49900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9150902E-02 2.0058652E-02 midg,1,midg; midg,igrid,midg 2.9279315E-03 -5.9544882E-03 1,midg,midg; igrid,midg,midg -9.8600402E-04 -1.6975614E-03 gauss-seidel spectral radius is 0.9983481 estimated iterations to convergence 195 setup time was (sec) 0.5100000 now iterating at: 14:19:30 rms-change max change #iterations 3.141346 156.9323 at 10iterations 1.351839 58.78681 at 20iterations 0.5908439 23.67139 at 30iterations 0.2560961 9.908653 at 40iterations 0.1104292 4.211824 at 50iterations 4.8011791E-02 1.919783 at 60iterations 2.0837335E-02 0.8118801 at 70iterations 9.0643112E-03 0.3495302 at 80iterations 3.9289142E-03 0.1497650 at 90iterations 1.7160961E-03 6.8485737E-02 at 100iterations 7.4228627E-04 2.7770996E-02 at 110iterations 3.2291297E-04 1.3216019E-02 at 120iterations finished qdiffx linear iterations at : 14:19:55 total time elapsed so far: 8.800000 # loops : 120 mean,max change (kT/e) : 3.2291297E-04 1.3216019E-02 energy calculations done at 8.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.940000 DelPhi exited at 14:19:56 8.939u 0.275s 0:31.55 29.1% 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 Tue Nov 22 2011 at 14:19:58 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.658568 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): -35.28200 10.11700 ymin,ymax (A): 1.296000 41.66000 zmin,zma (A): -1.630000 58.62800 x,y,z range (A): 45.39900 40.36400 60.25800 scale (grids/A): 2.658568 object centre (A): -12.58250 21.47800 28.49900 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.0260 centred at (gu) : 91.70135 87.44686 87.99946 assigned negative charge : -288.0262 centred at (gu) : 91.46822 88.07193 87.93972 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 115407 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16894 grid for indexing accessible points = 1.400000 m= 58225 mr = 82865 m= 20398 mr = 48087 m= 4122 mr = 16652 m= 463 mr = 3046 m= 17 mr = 279 m= 0 mr = 3 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 1153 time to turn everything in is 0.7000000 number of dielectric boundary points 47700 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 14644 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) : 1.772379 object centre at (A) : -12.58250 21.47800 28.49900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.3441539E-02 0.1415701 midg,1,midg; midg,igrid,midg -7.5250324E-03 -9.3788594E-02 1,midg,midg; igrid,midg,midg -3.4823738E-02 -4.6294723E-02 gauss-seidel spectral radius is 0.9991556 estimated iterations to convergence 272 setup time was (sec) 1.000000 now iterating at: 14:20:04 rms-change max change #iterations 7.641001 317.4517 at 10iterations 4.292930 128.3003 at 20iterations 2.408400 62.00054 at 30iterations 1.339148 39.92470 at 40iterations 0.7426926 18.78997 at 50iterations 0.4116169 9.722822 at 60iterations 0.2279474 5.361740 at 70iterations 0.1263561 2.897865 at 80iterations 6.9423497E-02 1.612444 at 90iterations 3.8442820E-02 0.7884865 at 100iterations 2.1297844E-02 0.4948158 at 110iterations 1.1792761E-02 0.2805843 at 120iterations 6.5141711E-03 0.1489258 at 130iterations 3.5893344E-03 8.2328796E-02 at 140iterations 1.9858794E-03 4.2314529E-02 at 150iterations 1.0957825E-03 2.5434494E-02 at 160iterations 6.0497422E-04 1.4426053E-02 at 170iterations 3.3319613E-04 7.9727173E-03 at 180iterations finished qdiffx linear iterations at : 14:20:43 total time elapsed so far: 13.92000 # loops : 180 mean,max change (kT/e) : 3.3319613E-04 7.9727173E-03 energy calculations done at 13.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.06000 DelPhi exited at 14:20:45 14.057u 0.304s 0:47.94 29.9% 0+0k 0+0io 0pf+0w