Sat Oct 15 13:15:27 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 Sat Oct 15 2011 at 13:15:27 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3313 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 0.5719886 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): -11.15500 51.08400 ymin,ymax (A): -12.75000 42.63500 zmin,zma (A): 19.64600 75.91000 x,y,z range (A): 62.23900 55.38500 56.26400 scale (grids/A): 0.5719886 object centre (A): 19.96450 14.94250 47.77800 number of atom coordinates read : 3313 total number of charged atoms : 3157 net assigned charge : 4.240018 assigned positive charge : 513.0617 centred at (gu) : 90.76456 89.74656 87.82642 assigned negative charge : -508.8231 centred at (gu) : 90.64600 89.84125 87.80644 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7328 nv = 96 ne = 84 npr = 63892 no. pairs analyzed = 63892 no. exposed pairs = 4489 no. arc points = 31489 no. surface atoms = 1496 nbur = 1817 mkacc time = 0.1800000 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 = 1.484000 m= 368 mr = 3686 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3981 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3084 ## 324 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9121 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7670706E-10 6.4342620E-10 midg,1,midg; midg,igrid,midg 2.6262743E-09 -1.0811653E-09 1,midg,midg; igrid,midg,midg -1.3426560E-09 3.5038619E-09 gauss-seidel spectral radius is 0.9842631 estimated iterations to convergence 66 setup time was (sec) 0.7100000 now iterating at: 13:15:28 rms-change max change #iterations 9.7384028E-02 19.30463 at 10iterations 7.2558559E-03 1.071398 at 20iterations 5.5933831E-04 8.3372116E-02 at 30iterations 4.5268502E-05 7.7371597E-03 at 40iterations 8.9745072E-06 1.2674332E-03 at 50iterations finished qdiffx linear iterations at : 13:15:32 total time elapsed so far: 5.220000 # loops : 50 mean,max change (kT/e) : 8.9745072E-06 1.2674332E-03 energy calculations done at 5.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.400000 DelPhi exited at 13:15:33 5.407u 0.435s 0:06.12 95.2% 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 Sat Oct 15 2011 at 13:15:33 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3313 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 1.715966 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): -11.15500 51.08400 ymin,ymax (A): -12.75000 42.63500 zmin,zma (A): 19.64600 75.91000 x,y,z range (A): 62.23900 55.38500 56.26400 scale (grids/A): 1.715966 object centre (A): 19.96450 14.94250 47.77800 number of atom coordinates read : 3313 total number of charged atoms : 3157 net assigned charge : 4.240018 assigned positive charge : 513.0617 centred at (gu) : 92.29282 89.23901 83.47836 assigned negative charge : -508.8231 centred at (gu) : 91.93764 89.52355 83.41898 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 80061 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31489 grid for indexing accessible points = 1.400000 m= 27240 mr = 53650 m= 3662 mr = 18554 m= 129 mr = 1816 m= 0 mr = 14 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6800000 number of dielectric boundary points 37058 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 268 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 24415 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) : 0.5719886 object centre at (A) : 19.96450 14.94250 47.77800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4411822E-02 5.6120665E-03 midg,1,midg; midg,igrid,midg 2.4574121E-02 -9.5673762E-03 1,midg,midg; igrid,midg,midg -9.5738238E-03 1.9313725E-02 gauss-seidel spectral radius is 0.9984044 estimated iterations to convergence 199 setup time was (sec) 1.050000 now iterating at: 13:15:34 rms-change max change #iterations 4.056293 165.8954 at 10iterations 1.781568 68.25433 at 20iterations 0.7877931 25.34206 at 30iterations 0.3469877 11.71554 at 40iterations 0.1539243 5.213488 at 50iterations 6.7936160E-02 2.307495 at 60iterations 3.0057564E-02 0.9434166 at 70iterations 1.3314017E-02 0.4631498 at 80iterations 5.9043169E-03 0.2084055 at 90iterations 2.6378774E-03 8.4571838E-02 at 100iterations 1.2043410E-03 4.0171862E-02 at 110iterations 5.9459219E-04 1.9371033E-02 at 120iterations finished qdiffx linear iterations at : 13:15:46 total time elapsed so far: 12.90000 # loops : 120 mean,max change (kT/e) : 5.9459219E-04 1.9371033E-02 energy calculations done at 12.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.07000 DelPhi exited at 13:15:47 13.077u 0.544s 0:13.95 97.5% 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 Sat Oct 15 2011 at 13:15:47 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3313 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 2.573949 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): -11.15500 51.08400 ymin,ymax (A): -12.75000 42.63500 zmin,zma (A): 19.64600 75.91000 x,y,z range (A): 62.23900 55.38500 56.26400 scale (grids/A): 2.573949 object centre (A): 19.96450 14.94250 47.77800 number of atom coordinates read : 3313 total number of charged atoms : 3157 net assigned charge : 4.240018 assigned positive charge : 513.0617 centred at (gu) : 93.43904 88.85841 80.21732 assigned negative charge : -508.8231 centred at (gu) : 92.90628 89.28522 80.12827 start vw surface at 0.1300000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 185836 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31489 grid for indexing accessible points = 1.400000 m= 90273 mr = 131927 m= 29600 mr = 70639 m= 5805 mr = 21854 m= 616 mr = 3841 m= 14 mr = 310 m= 0 mr = 2 time to grow re-entrant surface = 1.100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.750000 number of dielectric boundary points 83571 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 25211 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) : 1.715966 object centre at (A) : 19.96450 14.94250 47.77800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2843384 7.4317999E-02 midg,1,midg; midg,igrid,midg 0.3698358 -0.1501439 1,midg,midg; igrid,midg,midg 7.8292422E-02 0.2134890 gauss-seidel spectral radius is 0.9992197 estimated iterations to convergence 283 setup time was (sec) 2.150000 now iterating at: 13:15:49 rms-change max change #iterations 10.44361 326.3249 at 10iterations 6.180345 163.6417 at 20iterations 3.604464 84.56548 at 30iterations 2.097127 48.81676 at 40iterations 1.207942 30.87403 at 50iterations 0.6921211 15.21150 at 60iterations 0.3973885 8.616623 at 70iterations 0.2274934 5.010357 at 80iterations 0.1292903 2.731483 at 90iterations 7.4100584E-02 1.481255 at 100iterations 4.2115860E-02 0.9224951 at 110iterations 2.3990666E-02 0.4740038 at 120iterations 1.3655735E-02 0.2572927 at 130iterations 7.7778990E-03 0.1532869 at 140iterations 4.4621648E-03 9.0950012E-02 at 150iterations 2.5794881E-03 5.1069260E-02 at 160iterations 1.5243866E-03 3.1616211E-02 at 170iterations 9.4637583E-04 2.0310163E-02 at 180iterations finished qdiffx linear iterations at : 13:16:09 total time elapsed so far: 22.17000 # loops : 180 mean,max change (kT/e) : 9.4637583E-04 2.0310163E-02 energy calculations done at 22.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.34000 DelPhi exited at 13:16:10 22.342u 0.581s 0:23.24 98.6% 0+0k 0+0io 0pf+0w