Mon Oct 10 17:02:35 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 Mon Oct 10 2011 at 17:02:35 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2585 !!! WARNING: HIR 1202 has a net charge of 0.5140 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: 0.5636479 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): -17.69900 32.50200 ymin,ymax (A): -27.80000 29.33300 zmin,zma (A): 27.29600 90.45600 x,y,z range (A): 50.20100 57.13300 63.16000 scale (grids/A): 0.5636479 object centre (A): 7.401500 0.7665005 58.87600 number of atom coordinates read : 2585 total number of charged atoms : 2449 net assigned charge : 15.51402 assigned positive charge : 382.7218 centred at (gu) : 88.06501 90.72010 91.18664 assigned negative charge : -367.2086 centred at (gu) : 88.04641 90.77753 91.10071 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5448 nv = 96 ne = 84 npr = 51133 no. pairs analyzed = 51133 no. exposed pairs = 3409 no. arc points = 24364 no. surface atoms = 1157 nbur = 1428 mkacc time = 0.1400000 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 = 1.512000 m= 233 mr = 2690 m= 0 mr = 12 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 2979 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2466 ## 297 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 6929 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.5105638E-10 3.6529875E-09 midg,1,midg; midg,igrid,midg 2.0806568E-09 1.5035242E-09 1,midg,midg; igrid,midg,midg 2.6446152E-09 1.3203546E-09 gauss-seidel spectral radius is 0.9837365 estimated iterations to convergence 64 setup time was (sec) 0.6000000 now iterating at: 17:02:36 rms-change max change #iterations 7.9461992E-02 14.15674 at 10iterations 5.8784932E-03 0.9949846 at 20iterations 4.2047063E-04 8.3286285E-02 at 30iterations 3.0648098E-05 5.2042007E-03 at 40iterations 2.4877568E-06 4.2152405E-04 at 50iterations finished qdiffx linear iterations at : 17:02:41 total time elapsed so far: 4.960000 # loops : 50 mean,max change (kT/e) : 2.4877568E-06 4.2152405E-04 energy calculations done at 4.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.140000 DelPhi exited at 17:02:41 5.145u 0.453s 0:06.19 90.3% 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 17:02:41 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2585 !!! WARNING: HIR 1202 has a net charge of 0.5140 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: 1.690943 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): -17.69900 32.50200 ymin,ymax (A): -27.80000 29.33300 zmin,zma (A): 27.29600 90.45600 x,y,z range (A): 50.20100 57.13300 63.16000 scale (grids/A): 1.690943 object centre (A): 7.401500 0.7665005 58.87600 number of atom coordinates read : 2585 total number of charged atoms : 2449 net assigned charge : 15.51402 assigned positive charge : 382.7218 centred at (gu) : 84.19453 92.15986 93.55942 assigned negative charge : -367.2086 centred at (gu) : 84.13913 92.33233 93.30181 start vw surface at 0.1100000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 59347 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24364 grid for indexing accessible points = 1.400000 m= 18260 mr = 38950 m= 2137 mr = 12279 m= 80 mr = 1017 m= 4 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 27575 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 237 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 18882 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) : 0.5636479 object centre at (A) : 7.401500 0.7665005 58.87600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2297551E-03 2.3283293E-02 midg,1,midg; midg,igrid,midg 1.9732747E-02 1.6474849E-02 1,midg,midg; igrid,midg,midg 1.6186709E-02 9.7224461E-03 gauss-seidel spectral radius is 0.9982714 estimated iterations to convergence 191 setup time was (sec) 0.8900000 now iterating at: 17:02:44 rms-change max change #iterations 3.250586 144.7467 at 10iterations 1.371259 57.43286 at 20iterations 0.5831380 25.99280 at 30iterations 0.2478397 9.337989 at 40iterations 0.1051480 3.750889 at 50iterations 4.4949252E-02 1.636548 at 60iterations 1.9175356E-02 0.7451725 at 70iterations 8.1382906E-03 0.2971845 at 80iterations 3.4702183E-03 0.1419106 at 90iterations 1.4735548E-03 5.4138184E-02 at 100iterations 6.2865816E-04 2.4611473E-02 at 110iterations 2.6935199E-04 1.0480881E-02 at 120iterations finished qdiffx linear iterations at : 17:02:54 total time elapsed so far: 11.73000 # loops : 120 mean,max change (kT/e) : 2.6935199E-04 1.0480881E-02 energy calculations done at 11.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.91000 DelPhi exited at 17:02:55 11.919u 0.531s 0:13.82 90.0% 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 17:02:55 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2585 !!! WARNING: HIR 1202 has a net charge of 0.5140 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: 2.536415 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): -17.69900 32.50200 ymin,ymax (A): -27.80000 29.33300 zmin,zma (A): 27.29600 90.45600 x,y,z range (A): 50.20100 57.13300 63.16000 scale (grids/A): 2.536415 object centre (A): 7.401500 0.7665005 58.87600 number of atom coordinates read : 2585 total number of charged atoms : 2449 net assigned charge : 15.51402 assigned positive charge : 382.7218 centred at (gu) : 81.29154 93.23951 95.33902 assigned negative charge : -367.2086 centred at (gu) : 81.20864 93.49846 94.95267 start vw surface at 0.1200000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 138023 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24364 grid for indexing accessible points = 1.400000 m= 62452 mr = 95873 m= 18724 mr = 48706 m= 3373 mr = 13798 m= 324 mr = 2094 m= 14 mr = 148 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.270000 number of dielectric boundary points 62291 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 19575 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) : 1.690943 object centre at (A) : 7.401500 0.7665005 58.87600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.3743924E-02 0.3540758 midg,1,midg; midg,igrid,midg 0.1984433 0.1798855 1,midg,midg; igrid,midg,midg 0.1820894 0.1330482 gauss-seidel spectral radius is 0.9991589 estimated iterations to convergence 272 setup time was (sec) 1.640000 now iterating at: 17:02:57 rms-change max change #iterations 8.241343 326.0693 at 10iterations 4.655566 183.0754 at 20iterations 2.611840 74.77150 at 30iterations 1.461226 34.04105 at 40iterations 0.8160864 17.91191 at 50iterations 0.4545158 10.50033 at 60iterations 0.2526383 6.192839 at 70iterations 0.1401020 3.348558 at 80iterations 7.7635586E-02 1.883304 at 90iterations 4.3059904E-02 0.9533424 at 100iterations 2.3790035E-02 0.5074568 at 110iterations 1.3194656E-02 0.3010292 at 120iterations 7.2920392E-03 0.1580315 at 130iterations 4.0437351E-03 8.6906433E-02 at 140iterations 2.2355921E-03 5.3248167E-02 at 150iterations 1.2397848E-03 2.5684357E-02 at 160iterations 6.9002021E-04 1.4653206E-02 at 170iterations 3.8419239E-04 8.5649490E-03 at 180iterations finished qdiffx linear iterations at : 17:03:15 total time elapsed so far: 19.70000 # loops : 180 mean,max change (kT/e) : 3.8419239E-04 8.5649490E-03 energy calculations done at 19.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.86000 DelPhi exited at 17:03:16 19.863u 0.527s 0:21.30 95.6% 0+0k 0+0io 0pf+0w