Sun Oct 9 16:03:02 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 16:03:02 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 = 3189 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: 0.6292977 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): -15.16500 37.71900 ymin,ymax (A): 56.04000 107.8380 zmin,zma (A): -4.934000 51.63700 x,y,z range (A): 52.88400 51.79800 56.57100 scale (grids/A): 0.6292977 object centre (A): 11.27700 81.93900 23.35150 number of atom coordinates read : 3189 total number of charged atoms : 3044 net assigned charge : -2.499986 assigned positive charge : 475.7739 centred at (gu) : 89.68771 88.47042 91.08094 assigned negative charge : -478.2753 centred at (gu) : 89.74058 88.36948 91.15534 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8227 nv = 96 ne = 84 npr = 66299 no. pairs analyzed = 66299 no. exposed pairs = 3716 no. arc points = 26146 no. surface atoms = 1263 nbur = 1926 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 447 mr = 4598 m= 2 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3999 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2613 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 10246 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2858490E-09 -1.3150023E-08 midg,1,midg; midg,igrid,midg -1.8585972E-08 5.8573302E-09 1,midg,midg; igrid,midg,midg 3.4508900E-09 -7.5132904E-09 gauss-seidel spectral radius is 0.9869670 estimated iterations to convergence 72 setup time was (sec) 0.5500000 now iterating at: 16:03:03 rms-change max change #iterations 0.1534395 19.52096 at 10iterations 1.5071875E-02 2.104980 at 20iterations 1.7631867E-03 0.2905045 at 30iterations 3.3706147E-04 6.0131073E-02 at 40iterations 9.5097435E-05 1.7585754E-02 at 50iterations finished qdiffx linear iterations at : 16:03:05 total time elapsed so far: 3.010000 # loops : 50 mean,max change (kT/e) : 9.5097435E-05 1.7585754E-02 energy calculations done at 3.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.180000 DelPhi exited at 16:03:06 3.184u 0.139s 0:03.77 87.7% 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 16:03:06 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 = 3189 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.887893 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): -15.16500 37.71900 ymin,ymax (A): 56.04000 107.8380 zmin,zma (A): -4.934000 51.63700 x,y,z range (A): 52.88400 51.79800 56.57100 scale (grids/A): 1.887893 object centre (A): 11.27700 81.93900 23.35150 number of atom coordinates read : 3189 total number of charged atoms : 3044 net assigned charge : -2.499986 assigned positive charge : 475.7739 centred at (gu) : 89.06221 85.41054 93.24211 assigned negative charge : -478.2753 centred at (gu) : 89.22168 85.10809 93.46586 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 89685 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26146 grid for indexing accessible points = 1.400000 m= 32413 mr = 63379 m= 5661 mr = 23905 m= 381 mr = 3737 m= 4 mr = 150 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 665 time to turn everything in is 0.6100000 number of dielectric boundary points 36973 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 150 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 23889 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) : 0.6292977 object centre at (A) : 11.27700 81.93900 23.35150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9694425E-02 8.5984329E-03 midg,1,midg; midg,igrid,midg -2.4555506E-02 -4.9017430E-03 1,midg,midg; igrid,midg,midg -2.9190063E-02 -2.8438414E-02 gauss-seidel spectral radius is 0.9986576 estimated iterations to convergence 216 setup time was (sec) 0.8700000 now iterating at: 16:03:07 rms-change max change #iterations 4.731663 221.0661 at 10iterations 2.222642 65.34587 at 20iterations 1.047548 33.90121 at 30iterations 0.4942573 17.14373 at 40iterations 0.2338491 8.234913 at 50iterations 0.1100167 3.228905 at 60iterations 5.2167498E-02 1.413346 at 70iterations 2.4640581E-02 0.7665024 at 80iterations 1.1686740E-02 0.3632307 at 90iterations 5.5643409E-03 0.1753426 at 100iterations 2.6817529E-03 7.7733755E-02 at 110iterations 1.3046598E-03 3.9039612E-02 at 120iterations finished qdiffx linear iterations at : 16:03:13 total time elapsed so far: 7.160000 # loops : 120 mean,max change (kT/e) : 1.3046598E-03 3.9039612E-02 energy calculations done at 7.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.360000 DelPhi exited at 16:03:14 7.362u 0.161s 0:07.84 95.9% 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 16:03:14 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 = 3189 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: 2.831840 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): -15.16500 37.71900 ymin,ymax (A): 56.04000 107.8380 zmin,zma (A): -4.934000 51.63700 x,y,z range (A): 52.88400 51.79800 56.57100 scale (grids/A): 2.831840 object centre (A): 11.27700 81.93900 23.35150 number of atom coordinates read : 3189 total number of charged atoms : 3044 net assigned charge : -2.499986 assigned positive charge : 475.7739 centred at (gu) : 88.59315 83.11568 94.86290 assigned negative charge : -478.2753 centred at (gu) : 88.83246 82.66199 95.19876 start vw surface at 0.1500000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 207637 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26146 grid for indexing accessible points = 1.400000 m= 104352 mr = 153779 m= 39213 mr = 85439 m= 10474 mr = 31554 m= 1732 mr = 8150 m= 124 mr = 1246 m= 2 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 2071 time to turn everything in is 1.520000 number of dielectric boundary points 83307 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 24350 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) : 1.887893 object centre at (A) : 11.27700 81.93900 23.35150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5328928 0.2204318 midg,1,midg; midg,igrid,midg -0.2751880 -0.2012114 1,midg,midg; igrid,midg,midg -0.3736666 -0.3170489 gauss-seidel spectral radius is 0.9992749 estimated iterations to convergence 293 setup time was (sec) 1.820000 now iterating at: 16:03:16 rms-change max change #iterations 11.10668 298.3336 at 10iterations 6.553432 130.2559 at 20iterations 3.840588 75.74519 at 30iterations 2.251844 37.64069 at 40iterations 1.312328 23.78656 at 50iterations 0.7637501 14.42174 at 60iterations 0.4443751 8.845888 at 70iterations 0.2579234 4.275120 at 80iterations 0.1500323 2.545868 at 90iterations 8.6943984E-02 1.441021 at 100iterations 5.0415412E-02 0.8862991 at 110iterations 2.9295107E-02 0.4946957 at 120iterations 1.7013647E-02 0.2708168 at 130iterations 9.9297622E-03 0.1719383 at 140iterations 5.7937307E-03 9.5222473E-02 at 150iterations 3.4231406E-03 6.3301086E-02 at 160iterations 2.0519092E-03 3.6457062E-02 at 170iterations 1.2611325E-03 2.4887085E-02 at 180iterations finished qdiffx linear iterations at : 16:03:26 total time elapsed so far: 11.88000 # loops : 180 mean,max change (kT/e) : 1.2611325E-03 2.4887085E-02 energy calculations done at 11.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.08000 DelPhi exited at 16:03:27 12.086u 0.166s 0:12.53 97.6% 0+0k 0+0io 0pf+0w