Sun Oct 9 04:35:46 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 Sun Oct 9 2011 at 04:35:46 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2600 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: 0.6206848 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): -9.933001 35.99200 ymin,ymax (A): -2.055000 55.30100 zmin,zma (A): -23.95600 27.95900 x,y,z range (A): 45.92500 57.35600 51.91500 scale (grids/A): 0.6206848 object centre (A): 13.02950 26.62300 2.001500 number of atom coordinates read : 2600 total number of charged atoms : 2463 net assigned charge : 8.500016 assigned positive charge : 385.7844 centred at (gu) : 90.02772 90.16047 89.51226 assigned negative charge : -377.2855 centred at (gu) : 90.10458 90.05697 89.51971 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6800 nv = 96 ne = 84 npr = 51626 no. pairs analyzed = 51626 no. exposed pairs = 3578 no. arc points = 25519 no. surface atoms = 1181 nbur = 1419 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 361 mr = 3440 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.3000000 number of dielectric boundary points 3683 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2443 ## 254 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8200 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.2941307E-09 5.8543437E-09 midg,1,midg; midg,igrid,midg 8.5570120E-11 1.4218192E-08 1,midg,midg; igrid,midg,midg 1.1934291E-08 1.8776785E-09 gauss-seidel spectral radius is 0.9865652 estimated iterations to convergence 71 setup time was (sec) 0.5800000 now iterating at: 04:35:46 rms-change max change #iterations 0.1247442 18.54821 at 10iterations 1.1544894E-02 1.791124 at 20iterations 1.0742907E-03 0.1732292 at 30iterations 1.0190829E-04 1.4518738E-02 at 40iterations 1.1498611E-05 1.6269684E-03 at 50iterations finished qdiffx linear iterations at : 04:35:50 total time elapsed so far: 4.090000 # loops : 50 mean,max change (kT/e) : 1.1498611E-05 1.6269684E-03 energy calculations done at 4.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.280000 DelPhi exited at 04:35:51 4.282u 0.283s 0:04.85 94.0% 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 Sun Oct 9 2011 at 04:35:51 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2600 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: 1.862054 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): -9.933001 35.99200 ymin,ymax (A): -2.055000 55.30100 zmin,zma (A): -23.95600 27.95900 x,y,z range (A): 45.92500 57.35600 51.91500 scale (grids/A): 1.862054 object centre (A): 13.02950 26.62300 2.001500 number of atom coordinates read : 2600 total number of charged atoms : 2463 net assigned charge : 8.500016 assigned positive charge : 385.7844 centred at (gu) : 90.08241 90.48063 88.53580 assigned negative charge : -377.2855 centred at (gu) : 90.31345 90.17080 88.55866 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 72059 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25519 grid for indexing accessible points = 1.400000 m= 25433 mr = 47606 m= 3838 mr = 17930 m= 196 mr = 2107 m= 2 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 311 time to turn everything in is 0.5900000 number of dielectric boundary points 33819 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 157 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 19292 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) : 0.6206848 object centre at (A) : 13.02950 26.62300 2.001500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4990441E-02 2.5815901E-03 midg,1,midg; midg,igrid,midg 3.7854854E-03 3.1108195E-02 1,midg,midg; igrid,midg,midg 2.0875780E-02 6.4038546E-03 gauss-seidel spectral radius is 0.9985862 estimated iterations to convergence 211 setup time was (sec) 0.9300000 now iterating at: 04:35:52 rms-change max change #iterations 3.999280 178.8511 at 10iterations 1.837432 63.70020 at 20iterations 0.8473381 27.33823 at 30iterations 0.3911043 12.27065 at 40iterations 0.1797076 6.220489 at 50iterations 8.3113894E-02 3.327897 at 60iterations 3.8333077E-02 1.308029 at 70iterations 1.7684946E-02 0.5474033 at 80iterations 8.1800399E-03 0.2782717 at 90iterations 3.7738597E-03 0.1161242 at 100iterations 1.7541364E-03 6.1172485E-02 at 110iterations 8.0974080E-04 2.5037289E-02 at 120iterations finished qdiffx linear iterations at : 04:36:01 total time elapsed so far: 9.880000 # loops : 120 mean,max change (kT/e) : 8.0974080E-04 2.5037289E-02 energy calculations done at 9.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.09000 DelPhi exited at 04:36:01 10.096u 0.315s 0:10.73 96.9% 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 Sun Oct 9 2011 at 04:36:01 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2600 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: 2.793082 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): -9.933001 35.99200 ymin,ymax (A): -2.055000 55.30100 zmin,zma (A): -23.95600 27.95900 x,y,z range (A): 45.92500 57.35600 51.91500 scale (grids/A): 2.793082 object centre (A): 13.02950 26.62300 2.001500 number of atom coordinates read : 2600 total number of charged atoms : 2463 net assigned charge : 8.500016 assigned positive charge : 385.7844 centred at (gu) : 90.12334 90.72067 87.80354 assigned negative charge : -377.2855 centred at (gu) : 90.47013 90.25613 87.83804 start vw surface at 0.1800000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 166430 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25519 grid for indexing accessible points = 1.400000 m= 82312 mr = 116169 m= 29360 mr = 65259 m= 6561 mr = 22691 m= 823 mr = 4507 m= 49 mr = 495 m= 0 mr = 13 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 1081 time to turn everything in is 1.600000 number of dielectric boundary points 76401 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 19701 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) : 1.862054 object centre at (A) : 13.02950 26.62300 2.001500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4957078 7.0186086E-02 midg,1,midg; midg,igrid,midg -3.7711348E-02 0.4298625 1,midg,midg; igrid,midg,midg 0.2415142 7.4134551E-02 gauss-seidel spectral radius is 0.9992534 estimated iterations to convergence 289 setup time was (sec) 1.940000 now iterating at: 04:36:03 rms-change max change #iterations 9.595964 295.5447 at 10iterations 5.629622 159.7301 at 20iterations 3.282395 75.27931 at 30iterations 1.901821 69.28143 at 40iterations 1.101877 22.35509 at 50iterations 0.6361144 14.47222 at 60iterations 0.3665656 7.111466 at 70iterations 0.2107810 4.736740 at 80iterations 0.1213237 2.249203 at 90iterations 6.9674782E-02 1.456644 at 100iterations 3.9960228E-02 0.7823982 at 110iterations 2.2955775E-02 0.5929761 at 120iterations 1.3179758E-02 0.2771606 at 130iterations 7.5460132E-03 0.1487630 at 140iterations 4.3313531E-03 7.9368591E-02 at 150iterations 2.4809879E-03 4.6373367E-02 at 160iterations 1.4255595E-03 2.8383255E-02 at 170iterations 8.1772433E-04 1.7549515E-02 at 180iterations finished qdiffx linear iterations at : 04:36:17 total time elapsed so far: 15.58000 # loops : 180 mean,max change (kT/e) : 8.1772433E-04 1.7549515E-02 energy calculations done at 15.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.76000 DelPhi exited at 04:36:18 15.758u 0.280s 0:16.31 98.2% 0+0k 0+0io 0pf+0w