Mon Oct 10 14:03:01 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 Mon Oct 10 2011 at 14:03:02 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2125 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: 0.6906854 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): 8.254001 54.38200 ymin,ymax (A): -8.296000 35.67700 zmin,zma (A): -19.41500 32.12800 x,y,z range (A): 46.12800 43.97300 51.54300 scale (grids/A): 0.6906854 object centre (A): 31.31800 13.69050 6.356501 number of atom coordinates read : 2125 total number of charged atoms : 1985 net assigned charge : -5.999983 assigned positive charge : 318.2179 centred at (gu) : 90.93507 90.58296 88.88750 assigned negative charge : -324.2179 centred at (gu) : 90.79907 90.60988 88.69704 start vw surface at 0.1300000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6925 nv = 96 ne = 84 npr = 43682 no. pairs analyzed = 43682 no. exposed pairs = 2729 no. arc points = 19954 no. surface atoms = 913 nbur = 1212 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 451 mr = 3720 m= 3 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 37 time to turn everything in is 0.3300000 number of dielectric boundary points 3576 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1826 ## 139 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7736 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2646642E-07 2.5300086E-08 midg,1,midg; midg,igrid,midg -2.1337319E-08 -4.7745441E-08 1,midg,midg; igrid,midg,midg -6.7617066E-08 1.7059717E-08 gauss-seidel spectral radius is 0.9890913 estimated iterations to convergence 78 setup time was (sec) 0.6300000 now iterating at: 14:03:03 rms-change max change #iterations 0.1854705 26.00536 at 10iterations 2.1700829E-02 2.903370 at 20iterations 2.4652043E-03 0.3383551 at 30iterations 2.9236192E-04 4.5759678E-02 at 40iterations 3.3786291E-05 4.6539307E-03 at 50iterations finished qdiffx linear iterations at : 14:03:06 total time elapsed so far: 4.220000 # loops : 50 mean,max change (kT/e) : 3.3786291E-05 4.6539307E-03 energy calculations done at 4.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.440000 DelPhi exited at 14:03:07 4.449u 0.414s 0:05.33 90.9% 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 Mon Oct 10 2011 at 14:03:07 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2125 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: 2.072056 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): 8.254001 54.38200 ymin,ymax (A): -8.296000 35.67700 zmin,zma (A): -19.41500 32.12800 x,y,z range (A): 46.12800 43.97300 51.54300 scale (grids/A): 2.072056 object centre (A): 31.31800 13.69050 6.356501 number of atom coordinates read : 2125 total number of charged atoms : 1985 net assigned charge : -5.999983 assigned positive charge : 318.2179 centred at (gu) : 92.80501 91.74879 86.66251 assigned negative charge : -324.2179 centred at (gu) : 92.39709 91.82958 86.09108 start vw surface at 0.1400000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 72851 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19954 grid for indexing accessible points = 1.400000 m= 28179 mr = 48991 m= 5494 mr = 21076 m= 423 mr = 3672 m= 11 mr = 217 m= 0 mr = 2 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 1602 time to turn everything in is 0.7500000 number of dielectric boundary points 33000 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 58 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 15727 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) : 0.6906854 object centre at (A) : 31.31800 13.69050 6.356501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1156924 1.2365561E-02 midg,1,midg; midg,igrid,midg -1.7498957E-02 -2.3185335E-02 1,midg,midg; igrid,midg,midg -2.8076533E-02 4.7751614E-03 gauss-seidel spectral radius is 0.9987950 estimated iterations to convergence 228 setup time was (sec) 1.090000 now iterating at: 14:03:08 rms-change max change #iterations 4.504024 176.8328 at 10iterations 2.197506 72.65854 at 20iterations 1.075031 37.63250 at 30iterations 0.5257676 16.84658 at 40iterations 0.2583228 8.539362 at 50iterations 0.1259839 4.129086 at 60iterations 6.1728906E-02 1.879302 at 70iterations 3.0160330E-02 0.9334946 at 80iterations 1.4794466E-02 0.4865395 at 90iterations 7.2541414E-03 0.2131963 at 100iterations 3.5443336E-03 0.1155319 at 110iterations 1.7338037E-03 6.0558319E-02 at 120iterations finished qdiffx linear iterations at : 14:03:18 total time elapsed so far: 10.24000 # loops : 120 mean,max change (kT/e) : 1.7338037E-03 6.0558319E-02 energy calculations done at 10.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.47000 DelPhi exited at 14:03:18 10.472u 0.471s 0:11.36 96.3% 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 14:03:18 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2125 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: 3.108084 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): 8.254001 54.38200 ymin,ymax (A): -8.296000 35.67700 zmin,zma (A): -19.41500 32.12800 x,y,z range (A): 46.12800 43.97300 51.54300 scale (grids/A): 3.108084 object centre (A): 31.31800 13.69050 6.356501 number of atom coordinates read : 2125 total number of charged atoms : 1985 net assigned charge : -5.999983 assigned positive charge : 318.2179 centred at (gu) : 94.20741 92.62322 84.99365 assigned negative charge : -324.2179 centred at (gu) : 93.59557 92.74437 84.13654 start vw surface at 0.1300000 fill in re-entrant regions at 0.9600000 boundary points on vw surface= 167777 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19954 grid for indexing accessible points = 1.400000 m= 87260 mr = 118527 m= 35644 mr = 71364 m= 10292 mr = 29196 m= 1878 mr = 8072 m= 182 mr = 1364 m= 4 mr = 115 m= 0 mr = 2 time to grow re-entrant surface = 1.220000 no. cavity mid-points inaccessible to solvent = 5620 time to turn everything in is 2.310000 number of dielectric boundary points 74397 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.470000 number of grid points assigned charge 15880 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) : 2.072056 object centre at (A) : 31.31800 13.69050 6.356501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.213299 0.1467677 midg,1,midg; midg,igrid,midg -0.1666961 -0.2189115 1,midg,midg; igrid,midg,midg -0.2088530 -4.9936656E-02 gauss-seidel spectral radius is 0.9992913 estimated iterations to convergence 296 setup time was (sec) 2.680000 now iterating at: 14:03:21 rms-change max change #iterations 10.08182 497.2895 at 10iterations 5.895977 131.6903 at 20iterations 3.438970 89.73505 at 30iterations 2.001279 38.64899 at 40iterations 1.170218 23.68180 at 50iterations 0.6804342 17.17845 at 60iterations 0.3964787 8.298982 at 70iterations 0.2302487 4.320576 at 80iterations 0.1338421 2.425913 at 90iterations 7.7681601E-02 1.670477 at 100iterations 4.5129500E-02 0.9768162 at 110iterations 2.6295373E-02 0.4625641 at 120iterations 1.5194477E-02 0.2686996 at 130iterations 8.8577364E-03 0.1545162 at 140iterations 5.1508979E-03 9.1935158E-02 at 150iterations 2.9898081E-03 5.0851822E-02 at 160iterations 1.7356562E-03 3.0731201E-02 at 170iterations 1.0079230E-03 1.8678665E-02 at 180iterations finished qdiffx linear iterations at : 14:03:37 total time elapsed so far: 17.94000 # loops : 180 mean,max change (kT/e) : 1.0079230E-03 1.8678665E-02 energy calculations done at 17.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.17000 DelPhi exited at 14:03:38 18.172u 0.516s 0:20.14 92.7% 0+0k 0+0io 0pf+0w