Tue Oct 11 07:10:02 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 07:10:02 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3215 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 0.5905088 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): 0.3420000 48.39700 ymin,ymax (A): -8.095000 48.97300 zmin,zma (A): 0.9999999 61.28700 x,y,z range (A): 48.05500 57.06800 60.28700 scale (grids/A): 0.5905088 object centre (A): 24.36950 20.43900 31.14350 number of atom coordinates read : 3215 total number of charged atoms : 3062 net assigned charge : -3.099989 assigned positive charge : 483.4298 centred at (gu) : 89.71962 89.25542 90.77196 assigned negative charge : -486.5309 centred at (gu) : 89.63104 89.20049 90.72473 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7330 nv = 96 ne = 84 npr = 66724 no. pairs analyzed = 66724 no. exposed pairs = 3767 no. arc points = 25373 no. surface atoms = 1283 nbur = 1932 mkacc time = 0.1100000 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 = 1.456000 m= 350 mr = 4278 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.2400000 number of dielectric boundary points 3379 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2534 ## 260 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9312 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1500401E-09 7.7366491E-10 midg,1,midg; midg,igrid,midg -3.3637830E-09 7.4465700E-10 1,midg,midg; igrid,midg,midg -4.2589847E-09 1.8848638E-09 gauss-seidel spectral radius is 0.9852059 estimated iterations to convergence 67 setup time was (sec) 0.4300000 now iterating at: 07:10:02 rms-change max change #iterations 0.1148783 18.16898 at 10iterations 9.7030960E-03 1.305202 at 20iterations 9.5670542E-04 0.1473198 at 30iterations 1.6746121E-04 2.7679443E-02 at 40iterations 4.1876869E-05 7.0896149E-03 at 50iterations finished qdiffx linear iterations at : 07:10:05 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 4.1876869E-05 7.0896149E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 07:10:06 3.459u 0.171s 0:04.08 88.7% 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 Tue Oct 11 2011 at 07:10:06 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3215 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 1.771526 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): 0.3420000 48.39700 ymin,ymax (A): -8.095000 48.97300 zmin,zma (A): 0.9999999 61.28700 x,y,z range (A): 48.05500 57.06800 60.28700 scale (grids/A): 1.771526 object centre (A): 24.36950 20.43900 31.14350 number of atom coordinates read : 3215 total number of charged atoms : 3062 net assigned charge : -3.099989 assigned positive charge : 483.4298 centred at (gu) : 89.15789 87.76567 92.31502 assigned negative charge : -486.5309 centred at (gu) : 88.89269 87.60114 92.17374 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 80673 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25373 grid for indexing accessible points = 1.400000 m= 28890 mr = 58111 m= 3692 mr = 21734 m= 150 mr = 2247 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 981 time to turn everything in is 0.4000000 number of dielectric boundary points 31273 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 237 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 23832 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) : 0.5905088 object centre at (A) : 24.36950 20.43900 31.14350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0395502E-02 5.1362324E-03 midg,1,midg; midg,igrid,midg -1.2507706E-02 2.5328104E-03 1,midg,midg; igrid,midg,midg -2.0730514E-02 -1.1803322E-03 gauss-seidel spectral radius is 0.9984832 estimated iterations to convergence 204 setup time was (sec) 0.6100000 now iterating at: 07:10:07 rms-change max change #iterations 4.184332 152.5193 at 10iterations 1.888198 65.33487 at 20iterations 0.8492211 31.05120 at 30iterations 0.3838383 11.51622 at 40iterations 0.1726334 5.778015 at 50iterations 7.8106105E-02 2.542686 at 60iterations 3.5219125E-02 1.236389 at 70iterations 1.5899705E-02 0.4978294 at 80iterations 7.1724341E-03 0.2457047 at 90iterations 3.2536497E-03 9.5635414E-02 at 100iterations 1.4802988E-03 4.6707153E-02 at 110iterations 6.7523459E-04 2.1762848E-02 at 120iterations finished qdiffx linear iterations at : 07:10:14 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 6.7523459E-04 2.1762848E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 07:10:15 7.914u 0.190s 0:08.82 91.8% 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 Tue Oct 11 2011 at 07:10:15 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3215 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 2.657289 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): 0.3420000 48.39700 ymin,ymax (A): -8.095000 48.97300 zmin,zma (A): 0.9999999 61.28700 x,y,z range (A): 48.05500 57.06800 60.28700 scale (grids/A): 2.657289 object centre (A): 24.36950 20.43900 31.14350 number of atom coordinates read : 3215 total number of charged atoms : 3062 net assigned charge : -3.099989 assigned positive charge : 483.4298 centred at (gu) : 88.73673 86.64819 93.47244 assigned negative charge : -486.5309 centred at (gu) : 88.33881 86.40157 93.26062 start vw surface at 0.1200000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 187282 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25373 grid for indexing accessible points = 1.400000 m= 96056 mr = 140649 m= 32034 mr = 80027 m= 6240 mr = 25792 m= 607 mr = 4657 m= 19 mr = 393 m= 0 mr = 6 time to grow re-entrant surface = 0.5700000 no. cavity mid-points inaccessible to solvent = 3476 time to turn everything in is 1.020000 number of dielectric boundary points 70714 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 24491 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) : 1.771526 object centre at (A) : 24.36950 20.43900 31.14350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3920504 -0.2019318 midg,1,midg; midg,igrid,midg -0.2813257 2.4028735E-02 1,midg,midg; igrid,midg,midg -0.2337402 -4.2486366E-02 gauss-seidel spectral radius is 0.9992241 estimated iterations to convergence 283 setup time was (sec) 1.280000 now iterating at: 07:10:16 rms-change max change #iterations 10.11511 295.7964 at 10iterations 5.799395 130.2815 at 20iterations 3.321709 65.28152 at 30iterations 1.895158 36.66798 at 40iterations 1.079973 22.22804 at 50iterations 0.6158046 12.80338 at 60iterations 0.3498532 6.078993 at 70iterations 0.1990148 4.492447 at 80iterations 0.1125831 2.115061 at 90iterations 6.4062178E-02 1.112095 at 100iterations 3.6253721E-02 0.6528282 at 110iterations 2.0624764E-02 0.3613281 at 120iterations 1.1694156E-02 0.2186915 at 130iterations 6.6474904E-03 0.1255450 at 140iterations 3.7733563E-03 6.7558289E-02 at 150iterations 2.1534013E-03 3.9681435E-02 at 160iterations 1.2292302E-03 2.3468971E-02 at 170iterations 7.0788828E-04 1.1993408E-02 at 180iterations finished qdiffx linear iterations at : 07:10:28 total time elapsed so far: 12.79000 # loops : 180 mean,max change (kT/e) : 7.0788828E-04 1.1993408E-02 energy calculations done at 12.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.92000 DelPhi exited at 07:10:28 12.924u 0.180s 0:13.61 96.2% 0+0k 0+0io 0pf+0w