Sat Oct 8 11:38:38 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 Sat Oct 8 2011 at 11:38:38 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2525 !!! WARNING: HIZ 189 has a net charge of 0.2000 !!! WARNING: HIZ 193 has a net charge of 0.2000 !!! WARNING: HIZ 199 has a net charge of 0.2000 !!! WARNING: ZN5 517 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: 0.6102892 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): -18.16800 25.27200 ymin,ymax (A): -14.54500 43.78800 zmin,zma (A): 85.68700 136.4520 x,y,z range (A): 43.44000 58.33300 50.76500 scale (grids/A): 0.6102892 object centre (A): 3.552000 14.62150 111.0695 number of atom coordinates read : 2525 total number of charged atoms : 2385 net assigned charge : -1.499990 assigned positive charge : 386.2110 centred at (gu) : 90.99039 89.09583 90.26925 assigned negative charge : -387.7115 centred at (gu) : 90.89688 89.01772 90.38114 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6130 nv = 96 ne = 84 npr = 51958 no. pairs analyzed = 51958 no. exposed pairs = 2965 no. arc points = 21274 no. surface atoms = 995 nbur = 1530 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 307 mr = 3375 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.3500000 number of dielectric boundary points 3018 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2114 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7582 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.3440318E-09 -6.9337092E-09 midg,1,midg; midg,igrid,midg -5.8987237E-09 2.4164464E-09 1,midg,midg; igrid,midg,midg -4.4716781E-09 4.6888107E-09 gauss-seidel spectral radius is 0.9860893 estimated iterations to convergence 69 setup time was (sec) 0.6600000 now iterating at: 11:38:39 rms-change max change #iterations 0.1195182 18.25683 at 10iterations 1.0641748E-02 1.680662 at 20iterations 9.1495184E-04 0.1370811 at 30iterations 8.2390659E-05 1.4454365E-02 at 40iterations 7.2133207E-06 1.1005402E-03 at 50iterations finished qdiffx linear iterations at : 11:38:43 total time elapsed so far: 5.090000 # loops : 50 mean,max change (kT/e) : 7.2133207E-06 1.1005402E-03 energy calculations done at 5.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.280000 DelPhi exited at 11:38:44 5.286u 0.435s 0:06.09 93.7% 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 8 2011 at 11:38:44 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2525 !!! WARNING: HIZ 189 has a net charge of 0.2000 !!! WARNING: HIZ 193 has a net charge of 0.2000 !!! WARNING: HIZ 199 has a net charge of 0.2000 !!! WARNING: ZN5 517 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: 1.830868 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): -18.16800 25.27200 ymin,ymax (A): -14.54500 43.78800 zmin,zma (A): 85.68700 136.4520 x,y,z range (A): 43.44000 58.33300 50.76500 scale (grids/A): 1.830868 object centre (A): 3.552000 14.62150 111.0695 number of atom coordinates read : 2525 total number of charged atoms : 2385 net assigned charge : -1.499990 assigned positive charge : 386.2110 centred at (gu) : 92.97069 87.28696 90.80740 assigned negative charge : -387.7115 centred at (gu) : 92.69038 87.05287 91.14317 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 66824 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21274 grid for indexing accessible points = 1.400000 m= 22131 mr = 46350 m= 3131 mr = 16025 m= 199 mr = 1922 m= 1 mr = 113 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 2808 time to turn everything in is 0.6400000 number of dielectric boundary points 27876 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 176 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 18648 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) : 0.6102892 object centre at (A) : 3.552000 14.62150 111.0695 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6246594E-02 4.3152990E-03 midg,1,midg; midg,igrid,midg -2.2852140E-02 -6.2924703E-03 1,midg,midg; igrid,midg,midg -8.5081449E-03 -2.3371365E-03 gauss-seidel spectral radius is 0.9985117 estimated iterations to convergence 206 setup time was (sec) 1.010000 now iterating at: 11:38:45 rms-change max change #iterations 3.899090 151.4691 at 10iterations 1.758131 64.05989 at 20iterations 0.7976625 29.91199 at 30iterations 0.3618243 12.05789 at 40iterations 0.1635733 5.722987 at 50iterations 7.4254908E-02 2.511815 at 60iterations 3.3597317E-02 1.228638 at 70iterations 1.5193630E-02 0.5276680 at 80iterations 6.8834303E-03 0.2315722 at 90iterations 3.1154747E-03 0.1110263 at 100iterations 1.4131134E-03 5.2319527E-02 at 110iterations 6.4219517E-04 2.1043897E-02 at 120iterations finished qdiffx linear iterations at : 11:38:56 total time elapsed so far: 11.79000 # loops : 120 mean,max change (kT/e) : 6.4219517E-04 2.1043897E-02 energy calculations done at 11.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.96000 DelPhi exited at 11:38:57 11.967u 0.573s 0:13.16 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 8 2011 at 11:38:57 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2525 !!! WARNING: HIZ 189 has a net charge of 0.2000 !!! WARNING: HIZ 193 has a net charge of 0.2000 !!! WARNING: HIZ 199 has a net charge of 0.2000 !!! WARNING: ZN5 517 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: 2.746301 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): -18.16800 25.27200 ymin,ymax (A): -14.54500 43.78800 zmin,zma (A): 85.68700 136.4520 x,y,z range (A): 43.44000 58.33300 50.76500 scale (grids/A): 2.746301 object centre (A): 3.552000 14.62150 111.0695 number of atom coordinates read : 2525 total number of charged atoms : 2385 net assigned charge : -1.499990 assigned positive charge : 386.2110 centred at (gu) : 94.45601 85.93047 91.21107 assigned negative charge : -387.7115 centred at (gu) : 94.03562 85.57920 91.71468 start vw surface at 0.1500000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 155052 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21274 grid for indexing accessible points = 1.400000 m= 74604 mr = 112900 m= 23974 mr = 60620 m= 5489 mr = 18791 m= 916 mr = 4112 m= 60 mr = 729 m= 0 mr = 16 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 9705 time to turn everything in is 1.520000 number of dielectric boundary points 62927 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 19078 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) : 1.830868 object centre at (A) : 3.552000 14.62150 111.0695 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4161277 7.9538964E-02 midg,1,midg; midg,igrid,midg -0.1422731 -0.1168038 1,midg,midg; igrid,midg,midg -8.2072884E-02 -6.4218029E-02 gauss-seidel spectral radius is 0.9992192 estimated iterations to convergence 283 setup time was (sec) 1.940000 now iterating at: 11:39:00 rms-change max change #iterations 9.255176 330.1581 at 10iterations 5.293479 143.6361 at 20iterations 3.006925 63.52639 at 30iterations 1.702292 33.17287 at 40iterations 0.9646902 19.85201 at 50iterations 0.5453532 11.41766 at 60iterations 0.3084321 5.980576 at 70iterations 0.1743560 3.575912 at 80iterations 9.8409824E-02 1.888576 at 90iterations 5.5721652E-02 1.035138 at 100iterations 3.1451426E-02 0.6467094 at 110iterations 1.7790601E-02 0.3659577 at 120iterations 1.0050948E-02 0.2130392 at 130iterations 5.6633870E-03 0.1050816 at 140iterations 3.2060319E-03 6.7211151E-02 at 150iterations 1.8097344E-03 3.7826538E-02 at 160iterations 1.0235833E-03 2.1694183E-02 at 170iterations 5.7788705E-04 1.0912418E-02 at 180iterations finished qdiffx linear iterations at : 11:39:17 total time elapsed so far: 19.74000 # loops : 180 mean,max change (kT/e) : 5.7788705E-04 1.0912418E-02 energy calculations done at 19.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.93000 DelPhi exited at 11:39:18 19.930u 0.479s 0:20.75 98.3% 0+0k 0+0io 0pf+0w