Sat Oct 8 22:17:04 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+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 Sat Oct 8 2011 at 22:17:04 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2263 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 0.6566085 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): -15.39900 27.94000 ymin,ymax (A): -11.48600 41.89700 zmin,zma (A): 0.1090001 54.32700 x,y,z range (A): 43.33900 53.38300 54.21800 scale (grids/A): 0.6566085 object centre (A): 6.270501 15.20550 27.21800 number of atom coordinates read : 2263 total number of charged atoms : 2129 net assigned charge : 11.01403 assigned positive charge : 331.5226 centred at (gu) : 88.45789 91.20695 89.33600 assigned negative charge : -320.5093 centred at (gu) : 88.58165 91.20441 89.34534 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6799 nv = 96 ne = 84 npr = 45057 no. pairs analyzed = 45057 no. exposed pairs = 3000 no. arc points = 20903 no. surface atoms = 1008 nbur = 1255 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 455 mr = 3664 m= 2 mr = 47 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 0.2700000 number of dielectric boundary points 3545 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2002 ## 180 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7814 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0307817E-08 2.0757852E-08 midg,1,midg; midg,igrid,midg 1.9423460E-08 3.2550446E-08 1,midg,midg; igrid,midg,midg 5.9726240E-08 4.9515179E-09 gauss-seidel spectral radius is 0.9879566 estimated iterations to convergence 74 setup time was (sec) 0.4700000 now iterating at: 22:17:05 rms-change max change #iterations 0.1500410 24.38788 at 10iterations 1.5834263E-02 2.240025 at 20iterations 1.6991080E-03 0.2567766 at 30iterations 2.0524759E-04 3.5903931E-02 at 40iterations 3.0891148E-05 4.3182373E-03 at 50iterations finished qdiffx linear iterations at : 22:17:07 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 3.0891148E-05 4.3182373E-03 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 22:17:08 3.090u 0.143s 0:03.54 91.2% 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 Sat Oct 8 2011 at 22:17:08 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2263 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 1.969826 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): -15.39900 27.94000 ymin,ymax (A): -11.48600 41.89700 zmin,zma (A): 0.1090001 54.32700 x,y,z range (A): 43.33900 53.38300 54.21800 scale (grids/A): 1.969826 object centre (A): 6.270501 15.20550 27.21800 number of atom coordinates read : 2263 total number of charged atoms : 2129 net assigned charge : 11.01403 assigned positive charge : 331.5226 centred at (gu) : 85.37331 93.62079 88.00793 assigned negative charge : -320.5093 centred at (gu) : 85.74504 93.61347 88.03622 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 72083 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20903 grid for indexing accessible points = 1.400000 m= 27392 mr = 48842 m= 5255 mr = 19892 m= 385 mr = 3419 m= 7 mr = 157 m= 0 mr = 3 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 32809 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 136 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 16800 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) : 0.6566085 object centre at (A) : 6.270501 15.20550 27.21800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0027309E-02 4.5148220E-02 midg,1,midg; midg,igrid,midg 6.0960628E-02 3.0847015E-02 1,midg,midg; igrid,midg,midg 3.9614491E-02 -4.9188659E-03 gauss-seidel spectral radius is 0.9986919 estimated iterations to convergence 219 setup time was (sec) 0.8000000 now iterating at: 22:17:09 rms-change max change #iterations 4.106427 214.4003 at 10iterations 1.956438 67.08234 at 20iterations 0.9281122 29.19474 at 30iterations 0.4407749 16.55228 at 40iterations 0.2103371 6.490364 at 50iterations 9.9846877E-02 3.314175 at 60iterations 4.7454562E-02 1.557970 at 70iterations 2.2590365E-02 0.7531538 at 80iterations 1.0774261E-02 0.3638883 at 90iterations 5.1247315E-03 0.1848364 at 100iterations 2.4424896E-03 7.7064514E-02 at 110iterations 1.1690200E-03 4.0563583E-02 at 120iterations finished qdiffx linear iterations at : 22:17:15 total time elapsed so far: 6.910000 # loops : 120 mean,max change (kT/e) : 1.1690200E-03 4.0563583E-02 energy calculations done at 6.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.080000 DelPhi exited at 22:17:16 7.085u 0.153s 0:07.50 96.4% 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 Sat Oct 8 2011 at 22:17:16 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2263 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 2.954738 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): -15.39900 27.94000 ymin,ymax (A): -11.48600 41.89700 zmin,zma (A): 0.1090001 54.32700 x,y,z range (A): 43.33900 53.38300 54.21800 scale (grids/A): 2.954738 object centre (A): 6.270501 15.20550 27.21800 number of atom coordinates read : 2263 total number of charged atoms : 2129 net assigned charge : 11.01403 assigned positive charge : 331.5226 centred at (gu) : 83.06000 95.43101 87.01185 assigned negative charge : -320.5093 centred at (gu) : 83.61759 95.42016 87.05435 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 166421 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20903 grid for indexing accessible points = 1.400000 m= 85803 mr = 118763 m= 34281 mr = 69380 m= 9778 mr = 27282 m= 1695 mr = 7426 m= 129 mr = 1145 m= 7 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.310000 number of dielectric boundary points 74048 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 17032 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) : 1.969826 object centre at (A) : 6.270501 15.20550 27.21800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5769708 0.5223455 midg,1,midg; midg,igrid,midg 0.7444957 0.3173786 1,midg,midg; igrid,midg,midg 0.3567576 -4.4919506E-02 gauss-seidel spectral radius is 0.9992805 estimated iterations to convergence 294 setup time was (sec) 1.580000 now iterating at: 22:17:17 rms-change max change #iterations 9.718779 379.5966 at 10iterations 5.771990 132.0043 at 20iterations 3.420142 89.37591 at 30iterations 2.017342 41.45479 at 40iterations 1.182410 23.68774 at 50iterations 0.6939950 13.41503 at 60iterations 0.4056598 7.847973 at 70iterations 0.2362403 4.750307 at 80iterations 0.1378852 2.521076 at 90iterations 8.0150932E-02 1.464139 at 100iterations 4.6610855E-02 0.8690090 at 110iterations 2.7091010E-02 0.5197983 at 120iterations 1.5758969E-02 0.2778378 at 130iterations 9.1420617E-03 0.1590958 at 140iterations 5.3058118E-03 9.8020554E-02 at 150iterations 3.0833927E-03 5.5965424E-02 at 160iterations 1.7926808E-03 3.1364441E-02 at 170iterations 1.0451657E-03 1.8695831E-02 at 180iterations finished qdiffx linear iterations at : 22:17:27 total time elapsed so far: 10.96000 # loops : 180 mean,max change (kT/e) : 1.0451657E-03 1.8695831E-02 energy calculations done at 10.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.13000 DelPhi exited at 22:17:27 11.133u 0.165s 0:11.57 97.5% 0+0k 0+0io 0pf+0w