Sun Oct 9 08:14:00 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 08:14:00 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3671 !!! WARNING: NAP 1039 has a net charge of -2.0000 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: 0.5222161 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): -26.18100 22.94700 ymin,ymax (A): -23.61000 36.38200 zmin,zma (A): -18.03400 50.13700 x,y,z range (A): 49.12800 59.99200 68.17101 scale (grids/A): 0.5222161 object centre (A): -1.617000 6.386000 16.05150 number of atom coordinates read : 3671 total number of charged atoms : 3530 net assigned charge : 13.00004 assigned positive charge : 551.4261 centred at (gu) : 89.89339 87.96017 89.97335 assigned negative charge : -538.4278 centred at (gu) : 89.95495 87.88807 90.01791 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6489 nv = 96 ne = 84 npr = 72808 no. pairs analyzed = 72808 no. exposed pairs = 4925 no. arc points = 35613 no. surface atoms = 1605 nbur = 2066 mkacc time = 0.2100000 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 = 1.624000 m= 244 mr = 3139 m= 4 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 3584 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3419 ## 470 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 8613 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.5305620E-10 1.6717616E-10 midg,1,midg; midg,igrid,midg 1.2450742E-10 3.2013459E-10 1,midg,midg; igrid,midg,midg 5.1686910E-10 1.1100300E-10 gauss-seidel spectral radius is 0.9811721 estimated iterations to convergence 60 setup time was (sec) 0.7200000 now iterating at: 08:14:01 rms-change max change #iterations 6.6007271E-02 10.37116 at 10iterations 4.1008499E-03 0.6037941 at 20iterations 5.7079911E-04 8.4221363E-02 at 30iterations 1.6442109E-04 2.3477554E-02 at 40iterations 5.1799983E-05 7.3955059E-03 at 50iterations finished qdiffx linear iterations at : 08:14:05 total time elapsed so far: 4.010000 # loops : 50 mean,max change (kT/e) : 5.1799983E-05 7.3955059E-03 energy calculations done at 4.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.190000 DelPhi exited at 08:14:05 4.191u 0.269s 0:04.81 92.5% 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 08:14:05 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3671 !!! WARNING: NAP 1039 has a net charge of -2.0000 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: 1.566648 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): -26.18100 22.94700 ymin,ymax (A): -23.61000 36.38200 zmin,zma (A): -18.03400 50.13700 x,y,z range (A): 49.12800 59.99200 68.17101 scale (grids/A): 1.566648 object centre (A): -1.617000 6.386000 16.05150 number of atom coordinates read : 3671 total number of charged atoms : 3530 net assigned charge : 13.00004 assigned positive charge : 551.4261 centred at (gu) : 89.67910 83.87966 89.91906 assigned negative charge : -538.4278 centred at (gu) : 89.86456 83.66394 90.05367 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 71844 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35613 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 21735 mr = 47084 m= 2121 mr = 14333 m= 54 mr = 884 m= 2 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 451 time to turn everything in is 0.6600000 number of dielectric boundary points 33453 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 414 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 26695 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) : 0.5222161 object centre at (A) : -1.617000 6.386000 16.05150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9352635E-02 1.0071319E-02 midg,1,midg; midg,igrid,midg 4.6285139E-03 1.5976895E-02 1,midg,midg; igrid,midg,midg 1.0232423E-02 -7.5393618E-04 gauss-seidel spectral radius is 0.9981063 estimated iterations to convergence 183 setup time was (sec) 0.9600000 now iterating at: 08:14:07 rms-change max change #iterations 3.398568 161.1590 at 10iterations 1.387662 53.50364 at 20iterations 0.5682315 19.63608 at 30iterations 0.2319595 8.665600 at 40iterations 9.5239192E-02 3.904976 at 50iterations 3.8948260E-02 1.497084 at 60iterations 1.6035553E-02 0.5255737 at 70iterations 6.5961257E-03 0.2684109 at 80iterations 2.7399771E-03 9.7962260E-02 at 90iterations 1.1621085E-03 4.3436527E-02 at 100iterations 5.1254116E-04 1.8129349E-02 at 110iterations 2.4379519E-04 9.2812181E-03 at 120iterations finished qdiffx linear iterations at : 08:14:15 total time elapsed so far: 9.270000 # loops : 120 mean,max change (kT/e) : 2.4379519E-04 9.2812181E-03 energy calculations done at 9.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.440000 DelPhi exited at 08:14:15 9.440u 0.299s 0:10.04 96.9% 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 08:14:15 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3671 !!! WARNING: NAP 1039 has a net charge of -2.0000 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: 2.349973 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): -26.18100 22.94700 ymin,ymax (A): -23.61000 36.38200 zmin,zma (A): -18.03400 50.13700 x,y,z range (A): 49.12800 59.99200 68.17101 scale (grids/A): 2.349973 object centre (A): -1.617000 6.386000 16.05150 number of atom coordinates read : 3671 total number of charged atoms : 3530 net assigned charge : 13.00004 assigned positive charge : 551.4261 centred at (gu) : 89.51825 80.81934 89.87856 assigned negative charge : -538.4278 centred at (gu) : 89.79671 80.49579 90.08032 start vw surface at 0.1900000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 166981 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35613 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 75026 mr = 116172 m= 21124 mr = 57554 m= 3063 mr = 15383 m= 167 mr = 1751 m= 4 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.9399999 no. cavity mid-points inaccessible to solvent = 1555 time to turn everything in is 1.580000 number of dielectric boundary points 75463 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 50 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 28182 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) : 1.566648 object centre at (A) : -1.617000 6.386000 16.05150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2468411 0.1223302 midg,1,midg; midg,igrid,midg 0.1333924 0.3185475 1,midg,midg; igrid,midg,midg 0.1326783 -4.4532716E-02 gauss-seidel spectral radius is 0.9991362 estimated iterations to convergence 269 setup time was (sec) 1.900000 now iterating at: 08:14:18 rms-change max change #iterations 9.132192 306.4562 at 10iterations 5.179405 162.0955 at 20iterations 2.928061 73.14368 at 30iterations 1.642797 43.67107 at 40iterations 0.9152408 24.65845 at 50iterations 0.5101107 13.92024 at 60iterations 0.2823496 7.221346 at 70iterations 0.1565813 3.720131 at 80iterations 8.6460553E-02 2.114366 at 90iterations 4.7819573E-02 1.104889 at 100iterations 2.6343223E-02 0.6032467 at 110iterations 1.4506303E-02 0.3664265 at 120iterations 8.0023566E-03 0.1859779 at 130iterations 4.4011287E-03 0.1006927 at 140iterations 2.4212184E-03 5.7504654E-02 at 150iterations 1.3317585E-03 2.8297424E-02 at 160iterations 7.3217304E-04 1.6925097E-02 at 170iterations 4.0249509E-04 8.0757141E-03 at 180iterations finished qdiffx linear iterations at : 08:14:31 total time elapsed so far: 15.59000 # loops : 180 mean,max change (kT/e) : 4.0249509E-04 8.0757141E-03 energy calculations done at 15.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.76000 DelPhi exited at 08:14:32 15.762u 0.315s 0:16.36 98.2% 0+0k 0+0io 0pf+0w