Wed Dec 21 14:21:05 PST 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 Wed Dec 21 2011 at 14:21:05 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1906 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6111693 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): -23.64600 34.60300 ymin,ymax (A): -19.12200 20.44400 zmin,zma (A): -3.341000 39.07900 x,y,z range (A): 58.24900 39.56600 42.42000 scale (grids/A): 0.6111693 object centre (A): 5.478500 0.6610003 17.86900 number of atom coordinates read : 1906 total number of charged atoms : 1774 net assigned charge : 8.0007583E-02 assigned positive charge : 278.9201 centred at (gu) : 89.79407 90.35725 90.33971 assigned negative charge : -278.8403 centred at (gu) : 89.79067 90.42048 90.44063 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 4803 nv = 96 ne = 84 npr = 39375 no. pairs analyzed = 39375 no. exposed pairs = 2501 no. arc points = 17404 no. surface atoms = 853 nbur = 1053 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 238 mr = 2556 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 2473 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1782 ## 199 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 5840 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4728458E-09 -3.9822314E-09 midg,1,midg; midg,igrid,midg 2.2024580E-09 -2.4634961E-09 1,midg,midg; igrid,midg,midg -5.1920052E-11 1.9157012E-10 gauss-seidel spectral radius is 0.9860811 estimated iterations to convergence 69 setup time was (sec) 0.6100000 now iterating at: 14:21:06 rms-change max change #iterations 9.7136162E-02 16.44740 at 10iterations 8.8699898E-03 1.566206 at 20iterations 7.5241015E-04 0.1352062 at 30iterations 6.7881301E-05 1.1589050E-02 at 40iterations 6.0558427E-06 1.0652542E-03 at 50iterations finished qdiffx linear iterations at : 14:21:11 total time elapsed so far: 4.960000 # loops : 50 mean,max change (kT/e) : 6.0558427E-06 1.0652542E-03 energy calculations done at 4.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.150000 DelPhi exited at 14:21:12 5.157u 0.412s 0:06.36 87.4% 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 Wed Dec 21 2011 at 14:21:12 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1906 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.833508 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): -23.64600 34.60300 ymin,ymax (A): -19.12200 20.44400 zmin,zma (A): -3.341000 39.07900 x,y,z range (A): 58.24900 39.56600 42.42000 scale (grids/A): 1.833508 object centre (A): 5.478500 0.6610003 17.86900 number of atom coordinates read : 1906 total number of charged atoms : 1774 net assigned charge : 8.0007583E-02 assigned positive charge : 278.9201 centred at (gu) : 89.38203 91.07177 91.01921 assigned negative charge : -278.8403 centred at (gu) : 89.37216 91.26170 91.32210 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 52435 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17404 grid for indexing accessible points = 1.400000 m= 18366 mr = 35605 m= 2360 mr = 13386 m= 93 mr = 1301 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 22948 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 122 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 13849 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) : 0.6111693 object centre at (A) : 5.478500 0.6610003 17.86900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8240974E-03 -4.3371576E-03 midg,1,midg; midg,igrid,midg 1.5322081E-03 -1.0327185E-03 1,midg,midg; igrid,midg,midg 3.1267248E-02 2.1657556E-02 gauss-seidel spectral radius is 0.9984496 estimated iterations to convergence 201 setup time was (sec) 0.8900000 now iterating at: 14:21:13 rms-change max change #iterations 3.274951 159.2434 at 10iterations 1.453050 63.51484 at 20iterations 0.6466744 28.13247 at 30iterations 0.2872165 10.69662 at 40iterations 0.1280848 6.054962 at 50iterations 5.7132035E-02 2.249359 at 60iterations 2.5445726E-02 1.020424 at 70iterations 1.1274499E-02 0.4100351 at 80iterations 5.0161909E-03 0.1819382 at 90iterations 2.2420343E-03 8.7139130E-02 at 100iterations 1.0012370E-03 4.0500641E-02 at 110iterations 4.4585011E-04 1.6452789E-02 at 120iterations finished qdiffx linear iterations at : 14:21:23 total time elapsed so far: 11.28000 # loops : 120 mean,max change (kT/e) : 4.4585011E-04 1.6452789E-02 energy calculations done at 11.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.46000 DelPhi exited at 14:21:26 11.465u 0.476s 0:14.94 79.8% 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 Wed Dec 21 2011 at 14:21:27 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1906 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.750262 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): -23.64600 34.60300 ymin,ymax (A): -19.12200 20.44400 zmin,zma (A): -3.341000 39.07900 x,y,z range (A): 58.24900 39.56600 42.42000 scale (grids/A): 2.750262 object centre (A): 5.478500 0.6610003 17.86900 number of atom coordinates read : 1906 total number of charged atoms : 1774 net assigned charge : 8.0007583E-02 assigned positive charge : 278.9201 centred at (gu) : 89.07299 91.60767 91.52886 assigned negative charge : -278.8403 centred at (gu) : 89.05828 91.89261 91.98326 start vw surface at 0.1300000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 120996 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17404 grid for indexing accessible points = 1.400000 m= 60349 mr = 86058 m= 20375 mr = 49213 m= 3843 mr = 16033 m= 380 mr = 2700 m= 10 mr = 209 m= 2 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.250000 number of dielectric boundary points 51738 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 14192 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) : 1.833508 object centre at (A) : 5.478500 0.6610003 17.86900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1833030E-02 -2.5842437E-03 midg,1,midg; midg,igrid,midg 1.0366516E-02 2.3567908E-02 1,midg,midg; igrid,midg,midg 0.5578781 0.2714428 gauss-seidel spectral radius is 0.9991932 estimated iterations to convergence 278 setup time was (sec) 1.650000 now iterating at: 14:21:29 rms-change max change #iterations 7.882452 346.8712 at 10iterations 4.523857 122.2870 at 20iterations 2.577304 62.98825 at 30iterations 1.459370 32.69374 at 40iterations 0.8252478 19.07787 at 50iterations 0.4641981 9.943954 at 60iterations 0.2614970 6.079285 at 70iterations 0.1472647 3.609143 at 80iterations 8.2673334E-02 1.818041 at 90iterations 4.6412665E-02 1.003946 at 100iterations 2.6072055E-02 0.6147883 at 110iterations 1.4639392E-02 0.3384312 at 120iterations 8.1923530E-03 0.1823959 at 130iterations 4.5824107E-03 0.1043625 at 140iterations 2.5719928E-03 6.1602592E-02 at 150iterations 1.4428230E-03 3.1395674E-02 at 160iterations 8.0786942E-04 1.8342972E-02 at 170iterations 4.5272234E-04 9.7503662E-03 at 180iterations finished qdiffx linear iterations at : 14:21:45 total time elapsed so far: 16.92000 # loops : 180 mean,max change (kT/e) : 4.5272234E-04 9.7503662E-03 energy calculations done at 16.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.12000 DelPhi exited at 14:21:49 17.119u 0.568s 0:21.71 81.3% 0+0k 0+0io 0pf+0w