Sun Oct 9 14:21:43 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 Sun Oct 9 2011 at 14:21:44 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2724 !!! WARNING: HIR 41 has a net charge of 0.5140 !!! WARNING: SEP 187 has a net charge of -0.4750 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: 0.5492725 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): -2.320000 51.16100 ymin,ymax (A): -9.979000 38.24400 zmin,zma (A): -17.12400 47.68900 x,y,z range (A): 53.48100 48.22300 64.81300 scale (grids/A): 0.5492725 object centre (A): 24.42050 14.13250 15.28250 number of atom coordinates read : 2724 total number of charged atoms : 2583 net assigned charge : 4.539012 assigned positive charge : 416.2994 centred at (gu) : 89.89578 91.18029 89.14473 assigned negative charge : -411.7614 centred at (gu) : 89.80482 91.06726 89.22322 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5281 nv = 96 ne = 84 npr = 54636 no. pairs analyzed = 54636 no. exposed pairs = 3550 no. arc points = 25108 no. surface atoms = 1189 nbur = 1535 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 = 1.568000 m= 225 mr = 2614 m= 0 mr = 5 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 2887 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2571 ## 367 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 6949 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0460064E-09 -1.9449194E-10 midg,1,midg; midg,igrid,midg -3.6172543E-10 1.4495815E-09 1,midg,midg; igrid,midg,midg -3.4167880E-10 9.0785135E-10 gauss-seidel spectral radius is 0.9828880 estimated iterations to convergence 63 setup time was (sec) 0.5100000 now iterating at: 14:21:44 rms-change max change #iterations 7.3098533E-02 11.78268 at 10iterations 4.9265507E-03 0.9655304 at 20iterations 3.3668362E-04 6.0665131E-02 at 30iterations 2.2896731E-05 3.9520264E-03 at 40iterations 1.7885623E-06 3.5858154E-04 at 50iterations finished qdiffx linear iterations at : 14:21:47 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 1.7885623E-06 3.5858154E-04 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 14:21:47 3.090u 0.156s 0:03.53 91.7% 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 14:21:47 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2724 !!! WARNING: HIR 41 has a net charge of 0.5140 !!! WARNING: SEP 187 has a net charge of -0.4750 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: 1.647817 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): -2.320000 51.16100 ymin,ymax (A): -9.979000 38.24400 zmin,zma (A): -17.12400 47.68900 x,y,z range (A): 53.48100 48.22300 64.81300 scale (grids/A): 1.647817 object centre (A): 24.42050 14.13250 15.28250 number of atom coordinates read : 2724 total number of charged atoms : 2583 net assigned charge : 4.539012 assigned positive charge : 416.2994 centred at (gu) : 89.68669 93.54037 87.43357 assigned negative charge : -411.7614 centred at (gu) : 89.41439 93.20146 87.66957 start vw surface at 0.1500000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 58599 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25108 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 17680 mr = 39026 m= 1829 mr = 11587 m= 47 mr = 759 m= 0 mr = 4 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 62 time to turn everything in is 0.4200000 number of dielectric boundary points 26779 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 329 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 19844 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) : 0.5492725 object centre at (A) : 24.42050 14.13250 15.28250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1494418E-02 6.7243245E-03 midg,1,midg; midg,igrid,midg 4.4685995E-04 5.9101330E-03 1,midg,midg; igrid,midg,midg -2.0591583E-02 2.2701318E-03 gauss-seidel spectral radius is 0.9981956 estimated iterations to convergence 187 setup time was (sec) 0.6700000 now iterating at: 14:21:48 rms-change max change #iterations 3.265748 163.4230 at 10iterations 1.362299 60.06471 at 20iterations 0.5658503 22.17267 at 30iterations 0.2360016 8.500665 at 40iterations 9.8322272E-02 3.632094 at 50iterations 4.1103628E-02 1.655546 at 60iterations 1.7253935E-02 0.6469285 at 70iterations 7.1991291E-03 0.2780557 at 80iterations 3.0300056E-03 0.1142135 at 90iterations 1.2667537E-03 4.6485901E-02 at 100iterations 5.3289317E-04 2.1545410E-02 at 110iterations 2.2535332E-04 8.3999634E-03 at 120iterations finished qdiffx linear iterations at : 14:21:54 total time elapsed so far: 7.040000 # loops : 120 mean,max change (kT/e) : 2.2535332E-04 8.3999634E-03 energy calculations done at 7.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.230000 DelPhi exited at 14:21:55 7.232u 0.191s 0:07.75 95.7% 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 14:21:55 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2724 !!! WARNING: HIR 41 has a net charge of 0.5140 !!! WARNING: SEP 187 has a net charge of -0.4750 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: 2.471726 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): -2.320000 51.16100 ymin,ymax (A): -9.979000 38.24400 zmin,zma (A): -17.12400 47.68900 x,y,z range (A): 53.48100 48.22300 64.81300 scale (grids/A): 2.471726 object centre (A): 24.42050 14.13250 15.28250 number of atom coordinates read : 2724 total number of charged atoms : 2583 net assigned charge : 4.539012 assigned positive charge : 416.2994 centred at (gu) : 89.52987 95.31046 86.15025 assigned negative charge : -411.7614 centred at (gu) : 89.12151 94.80212 86.50421 start vw surface at 0.1600000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 135907 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25108 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 61500 mr = 95671 m= 17216 mr = 47579 m= 2797 mr = 12265 m= 226 mr = 1683 m= 4 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 237 time to turn everything in is 1.000000 number of dielectric boundary points 60367 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 20638 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) : 1.647817 object centre at (A) : 24.42050 14.13250 15.28250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7766243 0.1424745 midg,1,midg; midg,igrid,midg 1.3118750E-02 2.5300384E-02 1,midg,midg; igrid,midg,midg -0.3595658 3.6965068E-02 gauss-seidel spectral radius is 0.9991345 estimated iterations to convergence 269 setup time was (sec) 1.270000 now iterating at: 14:21:56 rms-change max change #iterations 8.509665 338.6087 at 10iterations 4.840197 146.1066 at 20iterations 2.727355 67.65636 at 30iterations 1.529409 45.13751 at 40iterations 0.8513169 19.95264 at 50iterations 0.4745462 12.16333 at 60iterations 0.2635722 6.045595 at 70iterations 0.1454774 3.393087 at 80iterations 8.0396451E-02 1.806168 at 90iterations 4.4268887E-02 1.216869 at 100iterations 2.4433361E-02 0.5141840 at 110iterations 1.3447831E-02 0.2840381 at 120iterations 7.4157272E-03 0.1648893 at 130iterations 4.0719495E-03 9.4505310E-02 at 140iterations 2.2409798E-03 5.2598953E-02 at 150iterations 1.2348650E-03 2.6634216E-02 at 160iterations 6.8313751E-04 1.5665054E-02 at 170iterations 3.7794522E-04 8.4304810E-03 at 180iterations finished qdiffx linear iterations at : 14:22:06 total time elapsed so far: 10.57000 # loops : 180 mean,max change (kT/e) : 3.7794522E-04 8.4304810E-03 energy calculations done at 10.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.75000 DelPhi exited at 14:22:06 10.748u 0.158s 0:11.18 97.4% 0+0k 0+0io 0pf+0w