Sun Oct 9 13:58:24 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 Sun Oct 9 2011 at 13:58:24 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 = 2392 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6907525 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): -6.965000 44.57300 ymin,ymax (A): 22.01400 73.26300 zmin,zma (A): 42.00100 84.90500 x,y,z range (A): 51.53800 51.24900 42.90400 scale (grids/A): 0.6907525 object centre (A): 18.80400 47.63850 63.45300 number of atom coordinates read : 2392 total number of charged atoms : 2251 net assigned charge : 4.500021 assigned positive charge : 364.8190 centred at (gu) : 89.87341 91.28194 90.36064 assigned negative charge : -360.3196 centred at (gu) : 89.87152 91.45185 90.43075 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7711 nv = 96 ne = 84 npr = 47797 no. pairs analyzed = 47797 no. exposed pairs = 3052 no. arc points = 21378 no. surface atoms = 1018 nbur = 1374 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 475 mr = 4207 m= 3 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3898 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2018 ## 187 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8738 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9857757E-08 -1.2309725E-09 midg,1,midg; midg,igrid,midg 7.0864409E-08 -5.3701545E-08 1,midg,midg; igrid,midg,midg 2.6352227E-08 2.6529458E-08 gauss-seidel spectral radius is 0.9891135 estimated iterations to convergence 78 setup time was (sec) 0.5200000 now iterating at: 13:58:25 rms-change max change #iterations 0.1927811 24.82655 at 10iterations 2.2792354E-02 2.947629 at 20iterations 3.0113827E-03 0.4367867 at 30iterations 6.1843835E-04 0.1008072 at 40iterations 1.9768291E-04 3.4898758E-02 at 50iterations finished qdiffx linear iterations at : 13:58:28 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 1.9768291E-04 3.4898758E-02 energy calculations done at 3.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 13:58:28 3.274u 0.169s 0:03.72 92.2% 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 13:58:28 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 = 2392 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: 2.072258 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): -6.965000 44.57300 ymin,ymax (A): 22.01400 73.26300 zmin,zma (A): 42.00100 84.90500 x,y,z range (A): 51.53800 51.24900 42.90400 scale (grids/A): 2.072258 object centre (A): 18.80400 47.63850 63.45300 number of atom coordinates read : 2392 total number of charged atoms : 2251 net assigned charge : 4.500021 assigned positive charge : 364.8190 centred at (gu) : 89.61963 93.84567 91.08142 assigned negative charge : -360.3196 centred at (gu) : 89.61427 94.35521 91.29209 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 81858 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21378 grid for indexing accessible points = 1.400000 m= 31434 mr = 56647 m= 5730 mr = 23372 m= 569 mr = 3719 m= 17 mr = 336 m= 0 mr = 2 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 264 time to turn everything in is 0.5800000 number of dielectric boundary points 35532 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 17859 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) : 0.6907525 object centre at (A) : 18.80400 47.63850 63.45300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9372295E-02 -8.5847819E-04 midg,1,midg; midg,igrid,midg 2.1385089E-02 -4.6067711E-02 1,midg,midg; igrid,midg,midg 5.9135307E-02 8.8587748E-03 gauss-seidel spectral radius is 0.9988209 estimated iterations to convergence 231 setup time was (sec) 0.8500000 now iterating at: 13:58:29 rms-change max change #iterations 4.831612 242.1954 at 10iterations 2.375599 75.16846 at 20iterations 1.175294 36.32892 at 30iterations 0.5810461 18.26561 at 40iterations 0.2865480 9.693359 at 50iterations 0.1424778 4.001831 at 60iterations 7.0428327E-02 2.158815 at 70iterations 3.4838479E-02 1.180062 at 80iterations 1.7365003E-02 0.5352974 at 90iterations 8.6751999E-03 0.2692151 at 100iterations 4.3998598E-03 0.1326370 at 110iterations 2.2954645E-03 7.6694489E-02 at 120iterations finished qdiffx linear iterations at : 13:58:35 total time elapsed so far: 7.120000 # loops : 120 mean,max change (kT/e) : 2.2954645E-03 7.6694489E-02 energy calculations done at 7.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.290000 DelPhi exited at 13:58:36 7.296u 0.199s 0:07.76 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 13:58:36 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 = 2392 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.108386 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): -6.965000 44.57300 ymin,ymax (A): 22.01400 73.26300 zmin,zma (A): 42.00100 84.90500 x,y,z range (A): 51.53800 51.24900 42.90400 scale (grids/A): 3.108386 object centre (A): 18.80400 47.63850 63.45300 number of atom coordinates read : 2392 total number of charged atoms : 2251 net assigned charge : 4.500021 assigned positive charge : 364.8190 centred at (gu) : 89.42933 95.76815 91.62203 assigned negative charge : -360.3196 centred at (gu) : 89.42135 96.53271 91.93813 start vw surface at 0.1400000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 188802 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21378 grid for indexing accessible points = 1.400000 m= 98614 mr = 136844 m= 38866 mr = 80768 m= 10737 mr = 31769 m= 2248 mr = 8183 m= 342 mr = 1723 m= 8 mr = 245 m= 0 mr = 0 time to grow re-entrant surface = 0.8899999 no. cavity mid-points inaccessible to solvent = 875 time to turn everything in is 1.840000 number of dielectric boundary points 80085 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 18003 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) : 2.072258 object centre at (A) : 18.80400 47.63850 63.45300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5874012 -0.1032396 midg,1,midg; midg,igrid,midg 0.2839275 -0.5673839 1,midg,midg; igrid,midg,midg 0.7019366 -0.1967549 gauss-seidel spectral radius is 0.9992996 estimated iterations to convergence 298 setup time was (sec) 2.140000 now iterating at: 13:58:38 rms-change max change #iterations 10.84094 358.5466 at 10iterations 6.417594 135.5433 at 20iterations 3.788740 68.48091 at 30iterations 2.236088 45.78762 at 40iterations 1.320352 22.57092 at 50iterations 0.7755413 13.91315 at 60iterations 0.4550605 7.357571 at 70iterations 0.2667963 4.202674 at 80iterations 0.1566131 2.604032 at 90iterations 9.1823332E-02 1.585144 at 100iterations 5.3885683E-02 1.057532 at 110iterations 3.1737462E-02 0.5598755 at 120iterations 1.8755555E-02 0.3055208 at 130iterations 1.1238089E-02 0.2165599 at 140iterations 6.8878573E-03 0.1258812 at 150iterations 4.3845372E-03 9.2399597E-02 at 160iterations 2.9242525E-03 6.0333252E-02 at 170iterations 2.0881887E-03 4.7697067E-02 at 180iterations finished qdiffx linear iterations at : 13:58:50 total time elapsed so far: 14.17000 # loops : 180 mean,max change (kT/e) : 2.0881887E-03 4.7697067E-02 energy calculations done at 14.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.34000 DelPhi exited at 13:58:51 14.343u 0.214s 0:14.84 98.0% 0+0k 0+0io 0pf+0w