Tue Oct 11 05:16:08 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+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 Tue Oct 11 2011 at 05:16:08 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2304 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: MG8 890 has a net charge of 1.4000 !!! WARNING: ZN8 891 has a net charge of 1.4000 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: 0.6859609 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): 16.35300 62.90500 ymin,ymax (A): -3.499000 33.61700 zmin,zma (A): 19.91900 71.81700 x,y,z range (A): 46.55200 37.11600 51.89800 scale (grids/A): 0.6859609 object centre (A): 39.62900 15.05900 45.86800 number of atom coordinates read : 2304 total number of charged atoms : 1982 net assigned charge : 9.000009 assigned positive charge : 325.1839 centred at (gu) : 91.23640 89.68541 89.24020 assigned negative charge : -316.1841 centred at (gu) : 91.34008 89.69136 89.17332 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6705 nv = 96 ne = 84 npr = 42122 no. pairs analyzed = 42122 no. exposed pairs = 2551 no. arc points = 17396 no. surface atoms = 865 nbur = 1439 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 454 mr = 3897 m= 4 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3193 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1628 ## 143 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7556 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8772376E-08 5.6686815E-08 midg,1,midg; midg,igrid,midg 5.0343477E-08 4.1155545E-08 1,midg,midg; igrid,midg,midg 6.0240339E-08 1.6674406E-08 gauss-seidel spectral radius is 0.9889301 estimated iterations to convergence 77 setup time was (sec) 0.5100000 now iterating at: 05:16:08 rms-change max change #iterations 0.1832374 24.82277 at 10iterations 2.1292729E-02 2.776009 at 20iterations 2.4887584E-03 0.3857651 at 30iterations 2.8673027E-04 3.6479950E-02 at 40iterations 3.5506539E-05 5.5236816E-03 at 50iterations finished qdiffx linear iterations at : 05:16:11 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 3.5506539E-05 5.5236816E-03 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 05:16:12 3.340u 0.203s 0:03.85 91.9% 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 Tue Oct 11 2011 at 05:16:12 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2304 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: MG8 890 has a net charge of 1.4000 !!! WARNING: ZN8 891 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.057883 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): 16.35300 62.90500 ymin,ymax (A): -3.499000 33.61700 zmin,zma (A): 19.91900 71.81700 x,y,z range (A): 46.55200 37.11600 51.89800 scale (grids/A): 2.057883 object centre (A): 39.62900 15.05900 45.86800 number of atom coordinates read : 2304 total number of charged atoms : 1982 net assigned charge : 9.000009 assigned positive charge : 325.1839 centred at (gu) : 93.70909 89.05630 87.72068 assigned negative charge : -316.1841 centred at (gu) : 94.02027 89.07440 87.51998 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 71765 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17396 grid for indexing accessible points = 1.400000 m= 28560 mr = 51330 m= 5240 mr = 21653 m= 450 mr = 3517 m= 6 mr = 229 m= 0 mr = 2 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 29290 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 90 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 15702 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) : 0.6859609 object centre at (A) : 39.62900 15.05900 45.86800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6874106E-02 4.7816984E-02 midg,1,midg; midg,igrid,midg 2.6546473E-02 2.1891365E-02 1,midg,midg; igrid,midg,midg 2.5044532E-02 2.4989719E-02 gauss-seidel spectral radius is 0.9987670 estimated iterations to convergence 226 setup time was (sec) 0.8300000 now iterating at: 05:16:13 rms-change max change #iterations 4.402901 232.0984 at 10iterations 2.146061 65.67007 at 20iterations 1.037133 33.21780 at 30iterations 0.5068618 15.44283 at 40iterations 0.2463617 7.495819 at 50iterations 0.1198796 3.697440 at 60iterations 5.8393359E-02 1.880512 at 70iterations 2.8401302E-02 0.8716164 at 80iterations 1.3880199E-02 0.4068928 at 90iterations 6.7776954E-03 0.1973076 at 100iterations 3.2849496E-03 9.6965790E-02 at 110iterations 1.6053641E-03 5.2377701E-02 at 120iterations finished qdiffx linear iterations at : 05:16:19 total time elapsed so far: 7.360000 # loops : 120 mean,max change (kT/e) : 1.6053641E-03 5.2377701E-02 energy calculations done at 7.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.550000 DelPhi exited at 05:16:20 7.549u 0.232s 0:08.31 93.5% 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 Tue Oct 11 2011 at 05:16:20 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2304 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: MG8 890 has a net charge of 1.4000 !!! WARNING: ZN8 891 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.086824 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): 16.35300 62.90500 ymin,ymax (A): -3.499000 33.61700 zmin,zma (A): 19.91900 71.81700 x,y,z range (A): 46.55200 37.11600 51.89800 scale (grids/A): 3.086824 object centre (A): 39.62900 15.05900 45.86800 number of atom coordinates read : 2304 total number of charged atoms : 1982 net assigned charge : 9.000009 assigned positive charge : 325.1839 centred at (gu) : 95.56367 88.58433 86.58104 assigned negative charge : -316.1841 centred at (gu) : 96.03045 88.61156 86.27999 start vw surface at 0.1600000 fill in re-entrant regions at 0.7600000 boundary points on vw surface= 165558 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17396 grid for indexing accessible points = 1.400000 m= 89525 mr = 123315 m= 35541 mr = 74779 m= 9869 mr = 29193 m= 1872 mr = 7728 m= 182 mr = 1355 m= 2 mr = 121 m= 0 mr = 2 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.650000 number of dielectric boundary points 66056 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 15856 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) : 2.057883 object centre at (A) : 39.62900 15.05900 45.86800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4149064 0.3692383 midg,1,midg; midg,igrid,midg 0.2423892 0.1938272 1,midg,midg; igrid,midg,midg 0.2311345 0.4683768 gauss-seidel spectral radius is 0.9992804 estimated iterations to convergence 294 setup time was (sec) 1.960000 now iterating at: 05:16:22 rms-change max change #iterations 9.984648 397.4856 at 10iterations 5.868956 135.3353 at 20iterations 3.441920 75.08473 at 30iterations 2.017034 40.29906 at 40iterations 1.178185 24.29889 at 50iterations 0.6892455 13.20510 at 60iterations 0.4016352 8.306068 at 70iterations 0.2342351 4.764725 at 80iterations 0.1363605 2.928192 at 90iterations 7.9180568E-02 1.414812 at 100iterations 4.6220962E-02 0.9135623 at 110iterations 2.6833175E-02 0.4842224 at 120iterations 1.5630271E-02 0.2781372 at 130iterations 9.1250790E-03 0.1934938 at 140iterations 5.3345449E-03 0.1007540 at 150iterations 3.1254408E-03 5.6190491E-02 at 160iterations 1.8539011E-03 3.8925171E-02 at 170iterations 1.1183399E-03 2.3559570E-02 at 180iterations finished qdiffx linear iterations at : 05:16:33 total time elapsed so far: 12.40000 # loops : 180 mean,max change (kT/e) : 1.1183399E-03 2.3559570E-02 energy calculations done at 12.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.57000 DelPhi exited at 05:16:33 12.575u 0.250s 0:13.44 95.3% 0+0k 0+0io 0pf+0w