Sun Oct 9 09:36:08 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 09:36:08 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2771 !!! WARNING: GLN 1020 has a net charge of -0.2720 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: 0.5603211 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): -80.69500 -33.28800 ymin,ymax (A): -34.93100 27.71200 zmin,zma (A): -55.13800 8.397000 x,y,z range (A): 47.40700 62.64300 63.53500 scale (grids/A): 0.5603211 object centre (A): -56.99150 -3.609500 -23.37050 number of atom coordinates read : 2771 total number of charged atoms : 2627 net assigned charge : 0.7280180 assigned positive charge : 408.2687 centred at (gu) : 89.47205 88.75571 88.94198 assigned negative charge : -407.5415 centred at (gu) : 89.47935 88.94436 88.91908 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5771 nv = 96 ne = 84 npr = 54606 no. pairs analyzed = 54606 no. exposed pairs = 3871 no. arc points = 27263 no. surface atoms = 1292 nbur = 1479 mkacc time = 0.1300000 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 = 1.540000 m= 260 mr = 2790 m= 1 mr = 14 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 0.3000000 number of dielectric boundary points 3228 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2733 ## 290 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7445 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3503002E-10 2.2423549E-10 midg,1,midg; midg,igrid,midg 2.6450173E-09 -1.4182989E-09 1,midg,midg; igrid,midg,midg 1.4776590E-10 -1.6671475E-11 gauss-seidel spectral radius is 0.9835626 estimated iterations to convergence 64 setup time was (sec) 0.5900000 now iterating at: 09:36:09 rms-change max change #iterations 7.9037055E-02 15.00620 at 10iterations 5.5213938E-03 1.123749 at 20iterations 4.0002537E-04 6.8576813E-02 at 30iterations 2.9066297E-05 4.8799515E-03 at 40iterations 2.1385131E-06 3.5095215E-04 at 50iterations finished qdiffx linear iterations at : 09:36:13 total time elapsed so far: 4.160000 # loops : 50 mean,max change (kT/e) : 2.1385131E-06 3.5095215E-04 energy calculations done at 4.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.350000 DelPhi exited at 09:36:13 4.351u 0.282s 0:04.92 94.1% 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 09:36:13 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2771 !!! WARNING: GLN 1020 has a net charge of -0.2720 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: 1.680963 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): -80.69500 -33.28800 ymin,ymax (A): -34.93100 27.71200 zmin,zma (A): -55.13800 8.397000 x,y,z range (A): 47.40700 62.64300 63.53500 scale (grids/A): 1.680963 object centre (A): -56.99150 -3.609500 -23.37050 number of atom coordinates read : 2771 total number of charged atoms : 2627 net assigned charge : 0.7280180 assigned positive charge : 408.2687 centred at (gu) : 88.41561 86.26688 86.82545 assigned negative charge : -407.5415 centred at (gu) : 88.43784 86.83257 86.75703 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 63183 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27263 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 20137 mr = 41001 m= 2287 mr = 13640 m= 76 mr = 1080 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 29955 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 252 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 20245 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) : 0.5603211 object centre at (A) : -56.99150 -3.609500 -23.37050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5287482E-02 6.8954541E-04 midg,1,midg; midg,igrid,midg 2.7039250E-02 -3.6144117E-03 1,midg,midg; igrid,midg,midg 7.6892003E-03 3.3169289E-03 gauss-seidel spectral radius is 0.9982823 estimated iterations to convergence 192 setup time was (sec) 0.8500000 now iterating at: 09:36:15 rms-change max change #iterations 3.364013 159.3552 at 10iterations 1.427271 59.19005 at 20iterations 0.6099741 24.11784 at 30iterations 0.2598639 9.215374 at 40iterations 0.1104280 4.801935 at 50iterations 4.7203057E-02 1.685766 at 60iterations 2.0052055E-02 0.8085136 at 70iterations 8.5589699E-03 0.3387680 at 80iterations 3.6607366E-03 0.1307793 at 90iterations 1.5661251E-03 5.5380821E-02 at 100iterations 6.6580495E-04 2.4894714E-02 at 110iterations 2.8568725E-04 1.1701107E-02 at 120iterations finished qdiffx linear iterations at : 09:36:23 total time elapsed so far: 9.740000 # loops : 120 mean,max change (kT/e) : 2.8568725E-04 1.1701107E-02 energy calculations done at 9.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.920000 DelPhi exited at 09:36:24 9.920u 0.322s 0:10.51 97.4% 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 Sun Oct 9 2011 at 09:36:24 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2771 !!! WARNING: GLN 1020 has a net charge of -0.2720 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: 2.521445 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): -80.69500 -33.28800 ymin,ymax (A): -34.93100 27.71200 zmin,zma (A): -55.13800 8.397000 x,y,z range (A): 47.40700 62.64300 63.53500 scale (grids/A): 2.521445 object centre (A): -56.99150 -3.609500 -23.37050 number of atom coordinates read : 2771 total number of charged atoms : 2627 net assigned charge : 0.7280180 assigned positive charge : 408.2687 centred at (gu) : 87.62321 84.40017 85.23788 assigned negative charge : -407.5415 centred at (gu) : 87.65678 85.24878 85.13560 start vw surface at 0.1400000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 146603 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27263 grid for indexing accessible points = 1.400000 m= 68129 mr = 100965 m= 20769 mr = 53018 m= 3630 mr = 15446 m= 286 mr = 2207 m= 10 mr = 112 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.240000 number of dielectric boundary points 67679 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 21002 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) : 1.680963 object centre at (A) : -56.99150 -3.609500 -23.37050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1921367 -5.0716516E-02 midg,1,midg; midg,igrid,midg 0.4991006 0.1002881 1,midg,midg; igrid,midg,midg 0.1130448 6.4380266E-02 gauss-seidel spectral radius is 0.9991707 estimated iterations to convergence 274 setup time was (sec) 1.610000 now iterating at: 09:36:26 rms-change max change #iterations 8.719753 309.0337 at 10iterations 4.991280 123.5292 at 20iterations 2.839745 72.61700 at 30iterations 1.604331 39.57212 at 40iterations 0.9019796 19.54095 at 50iterations 0.5068836 12.55042 at 60iterations 0.2838641 6.021240 at 70iterations 0.1586173 3.621517 at 80iterations 8.8376135E-02 2.060962 at 90iterations 4.9388677E-02 1.053745 at 100iterations 2.7478093E-02 0.5428858 at 110iterations 1.5281477E-02 0.3557291 at 120iterations 8.5272612E-03 0.1854343 at 130iterations 4.7456040E-03 0.1141758 at 140iterations 2.6389239E-03 5.3379536E-02 at 150iterations 1.4664459E-03 3.1243324E-02 at 160iterations 8.1531494E-04 1.7335892E-02 at 170iterations 4.5383870E-04 9.7064972E-03 at 180iterations finished qdiffx linear iterations at : 09:36:40 total time elapsed so far: 15.84000 # loops : 180 mean,max change (kT/e) : 4.5383870E-04 9.7064972E-03 energy calculations done at 15.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.03000 DelPhi exited at 09:36:41 16.029u 0.354s 0:16.73 97.8% 0+0k 0+0io 0pf+0w