Mon Oct 10 17:03:39 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 Mon Oct 10 2011 at 17:03:39 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5103 !!! WARNING: HIR 702 has a net charge of 0.5140 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5043207 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): -14.63200 47.69800 ymin,ymax (A): -28.15000 34.07500 zmin,zma (A): 15.54900 86.13900 x,y,z range (A): 62.33000 62.22500 70.59000 scale (grids/A): 0.5043207 object centre (A): 16.53300 2.962501 50.84400 number of atom coordinates read : 5103 total number of charged atoms : 4851 net assigned charge : 7.314042 assigned positive charge : 767.2842 centred at (gu) : 89.24924 90.08248 89.81933 assigned negative charge : -759.9758 centred at (gu) : 89.29543 90.03835 89.78170 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8160 nv = 96 ne = 84 npr = 103380 no. pairs analyzed = 103380 no. exposed pairs = 6404 no. arc points = 43820 no. surface atoms = 2171 nbur = 2932 mkacc time = 0.2400000 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 = 1.680000 m= 269 mr = 4205 m= 0 mr = 4 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 4220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4283 ## 672 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 10939 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4286473E-12 1.4892994E-10 midg,1,midg; midg,igrid,midg -1.5554157E-11 1.7350787E-10 1,midg,midg; igrid,midg,midg 2.1262649E-10 -1.6085936E-11 gauss-seidel spectral radius is 0.9799156 estimated iterations to convergence 58 setup time was (sec) 0.7500000 now iterating at: 17:03:40 rms-change max change #iterations 6.5508083E-02 8.973356 at 10iterations 5.5286493E-03 1.016426 at 20iterations 1.9868899E-03 0.4157677 at 30iterations 9.1786229E-04 0.1864014 at 40iterations 4.2783885E-04 8.4400177E-02 at 50iterations finished qdiffx linear iterations at : 17:03:43 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 4.2783885E-04 8.4400177E-02 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 17:03:44 3.620u 0.161s 0:04.93 76.6% 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 Mon Oct 10 2011 at 17:03:44 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5103 !!! WARNING: HIR 702 has a net charge of 0.5140 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.512962 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): -14.63200 47.69800 ymin,ymax (A): -28.15000 34.07500 zmin,zma (A): 15.54900 86.13900 x,y,z range (A): 62.33000 62.22500 70.59000 scale (grids/A): 1.512962 object centre (A): 16.53300 2.962501 50.84400 number of atom coordinates read : 5103 total number of charged atoms : 4851 net assigned charge : 7.314042 assigned positive charge : 767.2842 centred at (gu) : 87.74609 90.24566 89.45628 assigned negative charge : -759.9758 centred at (gu) : 87.88596 90.11459 89.34494 start vw surface at 0.2100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 93097 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43820 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 26286 mr = 64476 m= 2187 mr = 16951 m= 44 mr = 845 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7000000 number of dielectric boundary points 39342 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 623 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 36345 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) : 0.5043207 object centre at (A) : 16.53300 2.962501 50.84400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6574584E-02 1.0338640E-02 midg,1,midg; midg,igrid,midg 2.4451857E-04 1.8850447E-03 1,midg,midg; igrid,midg,midg 1.2640353E-02 -2.9893620E-03 gauss-seidel spectral radius is 0.9980865 estimated iterations to convergence 182 setup time was (sec) 1.040000 now iterating at: 17:03:45 rms-change max change #iterations 3.848585 163.0761 at 10iterations 1.564440 50.58043 at 20iterations 0.6406720 21.40273 at 30iterations 0.2616062 8.137148 at 40iterations 0.1067934 3.311231 at 50iterations 4.3849900E-02 1.365703 at 60iterations 1.8398942E-02 0.6143742 at 70iterations 8.1067896E-03 0.3293266 at 80iterations 4.1104550E-03 0.1768150 at 90iterations 2.5193922E-03 0.1100616 at 100iterations 1.7856391E-03 7.5637817E-02 at 110iterations 1.3507304E-03 5.6964874E-02 at 120iterations finished qdiffx linear iterations at : 17:03:52 total time elapsed so far: 8.260000 # loops : 120 mean,max change (kT/e) : 1.3507304E-03 5.6964874E-02 energy calculations done at 8.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.460000 DelPhi exited at 17:03:54 8.465u 0.233s 0:10.41 83.4% 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 Mon Oct 10 2011 at 17:03:54 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5103 !!! WARNING: HIR 702 has a net charge of 0.5140 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.269443 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): -14.63200 47.69800 ymin,ymax (A): -28.15000 34.07500 zmin,zma (A): 15.54900 86.13900 x,y,z range (A): 62.33000 62.22500 70.59000 scale (grids/A): 2.269443 object centre (A): 16.53300 2.962501 50.84400 number of atom coordinates read : 5103 total number of charged atoms : 4851 net assigned charge : 7.314042 assigned positive charge : 767.2842 centred at (gu) : 86.61877 90.36818 89.18419 assigned negative charge : -759.9758 centred at (gu) : 86.82906 90.17176 89.01722 start vw surface at 0.1900000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 217553 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43820 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 95501 mr = 158980 m= 22895 mr = 73737 m= 3065 mr = 15799 m= 171 mr = 1744 m= 5 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.750000 number of dielectric boundary points 88894 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 62 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 38696 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) : 1.512962 object centre at (A) : 16.53300 2.962501 50.84400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3332233 0.2309036 midg,1,midg; midg,igrid,midg 7.4421294E-02 -1.0502552E-02 1,midg,midg; igrid,midg,midg 0.2358715 -9.0554290E-02 gauss-seidel spectral radius is 0.9991616 estimated iterations to convergence 273 setup time was (sec) 2.090000 now iterating at: 17:03:57 rms-change max change #iterations 10.54603 253.1477 at 10iterations 6.086358 142.3256 at 20iterations 3.476788 77.61385 at 30iterations 1.974562 41.43443 at 40iterations 1.119360 28.71397 at 50iterations 0.6287114 12.78966 at 60iterations 0.3537790 7.509212 at 70iterations 0.1984054 3.782244 at 80iterations 0.1108534 2.285162 at 90iterations 6.1892219E-02 1.197849 at 100iterations 3.4658875E-02 0.7167473 at 110iterations 1.9350961E-02 0.3504333 at 120iterations 1.0770105E-02 0.2089767 at 130iterations 6.0387892E-03 0.1192589 at 140iterations 3.4065337E-03 7.0022583E-02 at 150iterations 1.9450343E-03 3.6933899E-02 at 160iterations 1.1503022E-03 2.5764465E-02 at 170iterations 7.1916718E-04 1.8337250E-02 at 180iterations finished qdiffx linear iterations at : 17:04:09 total time elapsed so far: 13.98000 # loops : 180 mean,max change (kT/e) : 7.1916718E-04 1.8337250E-02 energy calculations done at 13.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.18000 DelPhi exited at 17:04:10 14.178u 0.333s 0:15.71 92.2% 0+0k 0+0io 0pf+0w