Tue Oct 11 07:56:55 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 Tue Oct 11 2011 at 07:56:55 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2358 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: 0.6573603 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): -2.427000 51.72900 ymin,ymax (A): -22.13200 22.81500 zmin,zma (A): 8.816000 53.82200 x,y,z range (A): 54.15600 44.94700 45.00600 scale (grids/A): 0.6573603 object centre (A): 24.65100 0.3415003 31.31900 number of atom coordinates read : 2358 total number of charged atoms : 2222 net assigned charge : 5.500007 assigned positive charge : 353.2754 centred at (gu) : 89.40213 90.22654 90.15562 assigned negative charge : -347.7758 centred at (gu) : 89.42578 90.17902 89.97032 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6845 nv = 96 ne = 84 npr = 47999 no. pairs analyzed = 47999 no. exposed pairs = 2785 no. arc points = 19517 no. surface atoms = 937 nbur = 1421 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 373 mr = 3919 m= 5 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.2700000 number of dielectric boundary points 3262 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1921 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8062 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7748146E-08 4.4482565E-08 midg,1,midg; midg,igrid,midg 4.8294537E-09 2.1776374E-08 1,midg,midg; igrid,midg,midg 1.9052887E-08 8.0244931E-09 gauss-seidel spectral radius is 0.9879817 estimated iterations to convergence 74 setup time was (sec) 0.4800000 now iterating at: 07:56:55 rms-change max change #iterations 0.1513909 22.67588 at 10iterations 1.6197674E-02 2.336636 at 20iterations 1.7184148E-03 0.2657547 at 30iterations 1.8279074E-04 2.7511597E-02 at 40iterations 1.8785924E-05 2.8152466E-03 at 50iterations finished qdiffx linear iterations at : 07:56:58 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 1.8785924E-05 2.8152466E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 07:56:58 3.089u 0.144s 0:03.57 90.1% 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 07:56:58 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2358 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: 1.972081 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): -2.427000 51.72900 ymin,ymax (A): -22.13200 22.81500 zmin,zma (A): 8.816000 53.82200 x,y,z range (A): 54.15600 44.94700 45.00600 scale (grids/A): 1.972081 object centre (A): 24.65100 0.3415003 31.31900 number of atom coordinates read : 2358 total number of charged atoms : 2222 net assigned charge : 5.500007 assigned positive charge : 353.2754 centred at (gu) : 88.20602 90.67915 90.46664 assigned negative charge : -347.7758 centred at (gu) : 88.27722 90.53687 89.91083 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 73243 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19517 grid for indexing accessible points = 1.400000 m= 26990 mr = 51599 m= 4122 mr = 20229 m= 297 mr = 2550 m= 8 mr = 130 m= 0 mr = 2 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 2105 time to turn everything in is 0.5100000 number of dielectric boundary points 30150 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 139 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 17511 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) : 0.6573603 object centre at (A) : 24.65100 0.3415003 31.31900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2721063E-02 4.7967870E-02 midg,1,midg; midg,igrid,midg -5.3919741E-04 6.8695266E-03 1,midg,midg; igrid,midg,midg 2.5701661E-02 3.4382585E-02 gauss-seidel spectral radius is 0.9986967 estimated iterations to convergence 219 setup time was (sec) 0.7800000 now iterating at: 07:56:59 rms-change max change #iterations 4.227128 178.7047 at 10iterations 2.015962 69.78495 at 20iterations 0.9644141 32.38246 at 30iterations 0.4603769 15.65414 at 40iterations 0.2204468 7.194981 at 50iterations 0.1053846 3.373823 at 60iterations 5.0295085E-02 1.798500 at 70iterations 2.3963625E-02 0.7383137 at 80iterations 1.1453291E-02 0.3605537 at 90iterations 5.4421998E-03 0.1681519 at 100iterations 2.5990433E-03 8.4329605E-02 at 110iterations 1.2417194E-03 4.0445328E-02 at 120iterations finished qdiffx linear iterations at : 07:57:05 total time elapsed so far: 6.820000 # loops : 120 mean,max change (kT/e) : 1.2417194E-03 4.0445328E-02 energy calculations done at 6.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.000000 DelPhi exited at 07:57:06 7.005u 0.172s 0:07.58 94.5% 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 07:57:06 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2358 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: 2.958121 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): -2.427000 51.72900 ymin,ymax (A): -22.13200 22.81500 zmin,zma (A): 8.816000 53.82200 x,y,z range (A): 54.15600 44.94700 45.00600 scale (grids/A): 2.958121 object centre (A): 24.65100 0.3415003 31.31900 number of atom coordinates read : 2358 total number of charged atoms : 2222 net assigned charge : 5.500007 assigned positive charge : 353.2754 centred at (gu) : 87.30894 91.01875 90.69985 assigned negative charge : -347.7758 centred at (gu) : 87.41587 90.80536 89.86629 start vw surface at 0.1600000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 169279 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19517 grid for indexing accessible points = 1.400000 m= 87302 mr = 124660 m= 31571 mr = 72359 m= 7167 mr = 25605 m= 1160 mr = 5267 m= 98 mr = 834 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 7018 time to turn everything in is 1.280000 number of dielectric boundary points 67811 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 17772 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) : 1.972081 object centre at (A) : 24.65100 0.3415003 31.31900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3001364 0.4850867 midg,1,midg; midg,igrid,midg -3.3542402E-02 -8.1061302E-03 1,midg,midg; igrid,midg,midg 6.1867803E-02 0.1259947 gauss-seidel spectral radius is 0.9992629 estimated iterations to convergence 291 setup time was (sec) 1.560000 now iterating at: 07:57:08 rms-change max change #iterations 9.643144 444.1449 at 10iterations 5.587226 117.6077 at 20iterations 3.231472 66.49923 at 30iterations 1.867037 38.11692 at 40iterations 1.078875 19.17561 at 50iterations 0.6208618 12.13375 at 60iterations 0.3584778 6.407379 at 70iterations 0.2062693 3.642268 at 80iterations 0.1186597 2.093796 at 90iterations 6.8433039E-02 1.260180 at 100iterations 3.9269265E-02 0.7165956 at 110iterations 2.2610966E-02 0.4918556 at 120iterations 1.3010718E-02 0.2267504 at 130iterations 7.4908794E-03 0.1325159 at 140iterations 4.3230951E-03 8.0814362E-02 at 150iterations 2.4879014E-03 4.7330856E-02 at 160iterations 1.4341812E-03 2.4112225E-02 at 170iterations 8.3111250E-04 1.3931274E-02 at 180iterations finished qdiffx linear iterations at : 07:57:18 total time elapsed so far: 11.57000 # loops : 180 mean,max change (kT/e) : 8.3111250E-04 1.3931274E-02 energy calculations done at 11.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.74000 DelPhi exited at 07:57:18 11.741u 0.181s 0:12.45 95.7% 0+0k 0+0io 0pf+0w