Tue Oct 11 07:04:06 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 Tue Oct 11 2011 at 07:04:06 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3608 !!! WARNING: UMP 1153 has a net charge of -0.1000 !!! WARNING: CME 1 has a net charge of -0.1350 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: 0.5436941 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): -25.09600 31.45900 ymin,ymax (A): -24.17600 41.30200 zmin,zma (A): -16.19700 36.50000 x,y,z range (A): 56.55500 65.47800 52.69700 scale (grids/A): 0.5436941 object centre (A): 3.181500 8.563002 10.15150 number of atom coordinates read : 3608 total number of charged atoms : 3456 net assigned charge : 4.265024 assigned positive charge : 553.4486 centred at (gu) : 90.10279 89.34068 89.48055 assigned negative charge : -549.1860 centred at (gu) : 90.29265 89.41845 89.66090 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6764 nv = 96 ne = 84 npr = 73420 no. pairs analyzed = 73420 no. exposed pairs = 4226 no. arc points = 29927 no. surface atoms = 1433 nbur = 2175 mkacc time = 0.1200000 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 = 1.596000 m= 233 mr = 3649 m= 0 mr = 8 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.2400000 number of dielectric boundary points 3340 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3082 ## 445 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9005 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7821417E-09 -1.0122914E-09 midg,1,midg; midg,igrid,midg 9.6185215E-10 -3.0061365E-10 1,midg,midg; igrid,midg,midg 1.5906775E-09 -1.2634254E-09 gauss-seidel spectral radius is 0.9826045 estimated iterations to convergence 62 setup time was (sec) 0.4200000 now iterating at: 07:04:07 rms-change max change #iterations 8.2730040E-02 12.94427 at 10iterations 6.1058146E-03 1.070969 at 20iterations 1.4179152E-03 0.2403026 at 30iterations 6.3889695E-04 0.1117960 at 40iterations 2.9822814E-04 5.2523613E-02 at 50iterations finished qdiffx linear iterations at : 07:04:10 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 2.9822814E-04 5.2523613E-02 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 07:04:11 3.401u 0.182s 0:04.07 87.9% 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 Tue Oct 11 2011 at 07:04:11 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3608 !!! WARNING: UMP 1153 has a net charge of -0.1000 !!! WARNING: CME 1 has a net charge of -0.1350 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: 1.631082 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): -25.09600 31.45900 ymin,ymax (A): -24.17600 41.30200 zmin,zma (A): -16.19700 36.50000 x,y,z range (A): 56.55500 65.47800 52.69700 scale (grids/A): 1.631082 object centre (A): 3.181500 8.563002 10.15150 number of atom coordinates read : 3608 total number of charged atoms : 3456 net assigned charge : 4.265024 assigned positive charge : 553.4486 centred at (gu) : 90.30739 88.02139 88.44068 assigned negative charge : -549.1860 centred at (gu) : 90.87746 88.25517 88.98237 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 75509 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29927 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 22670 mr = 52120 m= 2337 mr = 15984 m= 56 mr = 1186 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 833 time to turn everything in is 0.3500000 number of dielectric boundary points 31281 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 378 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 26423 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) : 0.5436941 object centre at (A) : 3.181500 8.563002 10.15150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0450403E-02 -1.4858909E-02 midg,1,midg; midg,igrid,midg 2.2300798E-02 -7.7356771E-04 1,midg,midg; igrid,midg,midg 2.0478910E-02 -1.9517545E-02 gauss-seidel spectral radius is 0.9982446 estimated iterations to convergence 190 setup time was (sec) 0.5600000 now iterating at: 07:04:11 rms-change max change #iterations 3.764102 160.1080 at 10iterations 1.602420 54.35914 at 20iterations 0.6807262 25.77323 at 30iterations 0.2876829 9.777863 at 40iterations 0.1225340 4.080000 at 50iterations 5.2223638E-02 1.713428 at 60iterations 2.2477636E-02 0.8786049 at 70iterations 9.9568954E-03 0.3427205 at 80iterations 4.8087272E-03 0.1832762 at 90iterations 2.6563227E-03 9.9050522E-02 at 100iterations 1.7086141E-03 6.3741446E-02 at 110iterations 1.2344022E-03 4.3736219E-02 at 120iterations finished qdiffx linear iterations at : 07:04:18 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 1.2344022E-03 4.3736219E-02 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.670000 DelPhi exited at 07:04:19 7.672u 0.220s 0:08.37 94.2% 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 Tue Oct 11 2011 at 07:04:19 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3608 !!! WARNING: UMP 1153 has a net charge of -0.1000 !!! WARNING: CME 1 has a net charge of -0.1350 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: 2.446623 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): -25.09600 31.45900 ymin,ymax (A): -24.17600 41.30200 zmin,zma (A): -16.19700 36.50000 x,y,z range (A): 56.55500 65.47800 52.69700 scale (grids/A): 2.446623 object centre (A): 3.181500 8.563002 10.15150 number of atom coordinates read : 3608 total number of charged atoms : 3456 net assigned charge : 4.265024 assigned positive charge : 553.4486 centred at (gu) : 90.46062 87.03164 87.66060 assigned negative charge : -549.1860 centred at (gu) : 91.31607 87.38275 88.47353 start vw surface at 0.1000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 175378 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29927 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 79491 mr = 127166 m= 22423 mr = 63672 m= 3610 mr = 17250 m= 260 mr = 2425 m= 6 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 2658 time to turn everything in is 0.9000000 number of dielectric boundary points 70539 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 27608 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) : 1.631082 object centre at (A) : 3.181500 8.563002 10.15150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1100649 -0.2383956 midg,1,midg; midg,igrid,midg 0.2603124 6.1707787E-02 1,midg,midg; igrid,midg,midg 0.3668768 -0.3447617 gauss-seidel spectral radius is 0.9991641 estimated iterations to convergence 273 setup time was (sec) 1.130000 now iterating at: 07:04:20 rms-change max change #iterations 9.598710 286.3182 at 10iterations 5.394828 129.7520 at 20iterations 3.031104 66.56441 at 30iterations 1.696131 34.37173 at 40iterations 0.9476654 19.53257 at 50iterations 0.5272711 9.976720 at 60iterations 0.2941549 5.748005 at 70iterations 0.1632311 3.142168 at 80iterations 9.0851918E-02 1.792136 at 90iterations 5.0502893E-02 0.9589787 at 100iterations 2.8149102E-02 0.5253096 at 110iterations 1.5706651E-02 0.3080244 at 120iterations 8.8476148E-03 0.2017746 at 130iterations 5.0525004E-03 0.1165924 at 140iterations 2.9878614E-03 7.2212696E-02 at 150iterations 1.8713600E-03 4.1471481E-02 at 160iterations 1.2655655E-03 2.6983261E-02 at 170iterations 9.3295804E-04 2.0906448E-02 at 180iterations finished qdiffx linear iterations at : 07:04:32 total time elapsed so far: 12.34000 # loops : 180 mean,max change (kT/e) : 9.3295804E-04 2.0906448E-02 energy calculations done at 12.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.48000 DelPhi exited at 07:04:32 12.479u 0.207s 0:13.15 96.3% 0+0k 0+0io 0pf+0w