Tue Oct 11 08:28:51 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 Tue Oct 11 2011 at 08:28:51 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2838 !!! WARNING: GLU 295 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6368971 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): -5.708000 50.18800 ymin,ymax (A): 9.472000 62.04300 zmin,zma (A): 0.6320001 55.50400 x,y,z range (A): 55.89600 52.57100 54.87200 scale (grids/A): 0.6368971 object centre (A): 22.24000 35.75750 28.06800 number of atom coordinates read : 2838 total number of charged atoms : 2629 net assigned charge : 4.500018 assigned positive charge : 421.4866 centred at (gu) : 89.94771 90.19580 91.07613 assigned negative charge : -416.9872 centred at (gu) : 90.13082 90.11008 91.01498 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7294 nv = 96 ne = 84 npr = 59924 no. pairs analyzed = 59924 no. exposed pairs = 3313 no. arc points = 23016 no. surface atoms = 1125 nbur = 1713 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 419 mr = 4074 m= 4 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3595 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2300 ## 251 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 9019 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.7992746E-10 1.6238443E-08 midg,1,midg; midg,igrid,midg -3.8791477E-09 1.6338522E-08 1,midg,midg; igrid,midg,midg 2.6848307E-08 -1.5422945E-08 gauss-seidel spectral radius is 0.9872405 estimated iterations to convergence 72 setup time was (sec) 0.5100000 now iterating at: 08:28:51 rms-change max change #iterations 0.1507330 20.46582 at 10iterations 1.4924392E-02 2.449558 at 20iterations 1.4709758E-03 0.2096081 at 30iterations 1.6500540E-04 3.1517029E-02 at 40iterations 3.5294499E-05 6.5965652E-03 at 50iterations finished qdiffx linear iterations at : 08:28:54 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 3.5294499E-05 6.5965652E-03 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 08:28:54 3.160u 0.165s 0:03.73 89.0% 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 Oct 11 2011 at 08:28:54 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2838 !!! WARNING: GLU 295 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.910691 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): -5.708000 50.18800 ymin,ymax (A): 9.472000 62.04300 zmin,zma (A): 0.6320001 55.50400 x,y,z range (A): 55.89600 52.57100 54.87200 scale (grids/A): 1.910691 object centre (A): 22.24000 35.75750 28.06800 number of atom coordinates read : 2838 total number of charged atoms : 2629 net assigned charge : 4.500018 assigned positive charge : 421.4866 centred at (gu) : 89.84250 90.58651 93.22771 assigned negative charge : -416.9872 centred at (gu) : 90.39217 90.32988 93.04467 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77583 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23016 grid for indexing accessible points = 1.400000 m= 29252 mr = 53801 m= 5104 mr = 21896 m= 302 mr = 3229 m= 5 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 301 time to turn everything in is 0.5600000 number of dielectric boundary points 33224 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 163 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 20716 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) : 0.6368971 object centre at (A) : 22.24000 35.75750 28.06800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2322536E-02 8.1544667E-02 midg,1,midg; midg,igrid,midg -4.9649780E-03 -1.4707824E-03 1,midg,midg; igrid,midg,midg 6.8692967E-02 -6.5171428E-02 gauss-seidel spectral radius is 0.9986618 estimated iterations to convergence 217 setup time was (sec) 0.8200000 now iterating at: 08:28:55 rms-change max change #iterations 4.451626 183.7348 at 10iterations 2.109094 74.87382 at 20iterations 0.9900034 29.57509 at 30iterations 0.4699571 14.15910 at 40iterations 0.2221626 6.716107 at 50iterations 0.1053042 3.141987 at 60iterations 4.9701821E-02 1.558925 at 70iterations 2.3445250E-02 0.7199249 at 80iterations 1.1070389E-02 0.3668728 at 90iterations 5.2325930E-03 0.1513004 at 100iterations 2.4849942E-03 9.1427803E-02 at 110iterations 1.1867991E-03 3.7750244E-02 at 120iterations finished qdiffx linear iterations at : 08:29:02 total time elapsed so far: 7.420000 # loops : 120 mean,max change (kT/e) : 1.1867991E-03 3.7750244E-02 energy calculations done at 7.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.600000 DelPhi exited at 08:29:03 7.602u 0.161s 0:08.05 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 Tue Oct 11 2011 at 08:29:03 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2838 !!! WARNING: GLU 295 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.866037 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): -5.708000 50.18800 ymin,ymax (A): 9.472000 62.04300 zmin,zma (A): 0.6320001 55.50400 x,y,z range (A): 55.89600 52.57100 54.87200 scale (grids/A): 2.866037 object centre (A): 22.24000 35.75750 28.06800 number of atom coordinates read : 2838 total number of charged atoms : 2629 net assigned charge : 4.500018 assigned positive charge : 421.4866 centred at (gu) : 89.76372 90.87975 94.84145 assigned negative charge : -416.9872 centred at (gu) : 90.58811 90.49480 94.56689 start vw surface at 0.1800000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 179130 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23016 grid for indexing accessible points = 1.400000 m= 92314 mr = 130132 m= 36362 mr = 75944 m= 9347 mr = 29673 m= 1298 mr = 7006 m= 62 mr = 826 m= 2 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 1059 time to turn everything in is 1.410000 number of dielectric boundary points 74918 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 21032 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) : 1.910691 object centre at (A) : 22.24000 35.75750 28.06800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2657487 1.177125 midg,1,midg; midg,igrid,midg -2.4403412E-02 -0.1791901 1,midg,midg; igrid,midg,midg 1.258865 -0.8375533 gauss-seidel spectral radius is 0.9992638 estimated iterations to convergence 291 setup time was (sec) 1.680000 now iterating at: 08:29:04 rms-change max change #iterations 10.35193 385.8247 at 10iterations 6.059102 183.4478 at 20iterations 3.513194 83.79473 at 30iterations 2.042878 43.41322 at 40iterations 1.183039 22.50747 at 50iterations 0.6854360 11.92462 at 60iterations 0.3964730 6.947254 at 70iterations 0.2289788 4.149539 at 80iterations 0.1322992 2.618704 at 90iterations 7.6351456E-02 1.314610 at 100iterations 4.4012934E-02 0.7707596 at 110iterations 2.5375372E-02 0.4762402 at 120iterations 1.4637244E-02 0.2638588 at 130iterations 8.4320651E-03 0.1434140 at 140iterations 4.8808963E-03 8.6517334E-02 at 150iterations 2.8310630E-03 4.8261642E-02 at 160iterations 1.6501227E-03 2.9108524E-02 at 170iterations 9.7857206E-04 1.7410278E-02 at 180iterations finished qdiffx linear iterations at : 08:29:14 total time elapsed so far: 11.29000 # loops : 180 mean,max change (kT/e) : 9.7857206E-04 1.7410278E-02 energy calculations done at 11.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.46000 DelPhi exited at 08:29:15 11.465u 0.185s 0:11.98 97.1% 0+0k 0+0io 0pf+0w