Tue Oct 11 08:32:19 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 08:32:19 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 = 2081 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: 0.7198318 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): -20.75200 26.53600 ymin,ymax (A): -10.84000 26.15200 zmin,zma (A): -3.172000 46.28400 x,y,z range (A): 47.28800 36.99200 49.45600 scale (grids/A): 0.7198318 object centre (A): 2.892001 7.656001 21.55600 number of atom coordinates read : 2081 total number of charged atoms : 1953 net assigned charge : 6.500009 assigned positive charge : 316.0039 centred at (gu) : 89.23264 89.21877 90.87875 assigned negative charge : -309.5042 centred at (gu) : 89.08705 89.23780 90.94990 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7358 nv = 96 ne = 84 npr = 41982 no. pairs analyzed = 41982 no. exposed pairs = 2523 no. arc points = 17430 no. surface atoms = 864 nbur = 1217 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 513 mr = 4293 m= 2 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3512 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1533 ## 130 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7998 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0139290E-07 3.2686156E-08 midg,1,midg; midg,igrid,midg 1.0011419E-07 5.3804612E-08 1,midg,midg; igrid,midg,midg -2.4781446E-08 1.4382434E-07 gauss-seidel spectral radius is 0.9899357 estimated iterations to convergence 81 setup time was (sec) 0.4700000 now iterating at: 08:32:20 rms-change max change #iterations 0.2136971 29.86742 at 10iterations 2.7401436E-02 4.002676 at 20iterations 3.6061020E-03 0.4733219 at 30iterations 5.3088978E-04 6.5670013E-02 at 40iterations 1.0511745E-04 1.3912201E-02 at 50iterations finished qdiffx linear iterations at : 08:32:22 total time elapsed so far: 2.860000 # loops : 50 mean,max change (kT/e) : 1.0511745E-04 1.3912201E-02 energy calculations done at 2.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.030000 DelPhi exited at 08:32:23 3.031u 0.150s 0:03.58 88.8% 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 08:32:23 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 = 2081 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.159495 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): -20.75200 26.53600 ymin,ymax (A): -10.84000 26.15200 zmin,zma (A): -3.172000 46.28400 x,y,z range (A): 47.28800 36.99200 49.45600 scale (grids/A): 2.159495 object centre (A): 2.892001 7.656001 21.55600 number of atom coordinates read : 2081 total number of charged atoms : 1953 net assigned charge : 6.500009 assigned positive charge : 316.0039 centred at (gu) : 87.69807 87.65620 92.63612 assigned negative charge : -309.5042 centred at (gu) : 87.26128 87.71358 92.84985 start vw surface at 0.1900000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 77312 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17430 grid for indexing accessible points = 1.400000 m= 31752 mr = 55114 m= 6420 mr = 24258 m= 585 mr = 4352 m= 12 mr = 294 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 32063 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 59 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 15527 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) : 0.7198318 object centre at (A) : 2.892001 7.656001 21.55600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6222109E-02 6.3351654E-02 midg,1,midg; midg,igrid,midg 3.8588591E-02 5.4441877E-03 1,midg,midg; igrid,midg,midg 1.5600766E-02 3.7712671E-02 gauss-seidel spectral radius is 0.9988645 estimated iterations to convergence 235 setup time was (sec) 0.9000000 now iterating at: 08:32:24 rms-change max change #iterations 4.737629 196.3749 at 10iterations 2.367108 84.50363 at 20iterations 1.186629 41.00752 at 30iterations 0.5938925 17.44995 at 40iterations 0.2991926 10.24709 at 50iterations 0.1496444 4.415162 at 60iterations 7.5440116E-02 2.275997 at 70iterations 3.7913479E-02 1.079848 at 80iterations 1.9033883E-02 0.6078415 at 90iterations 9.5630558E-03 0.3227262 at 100iterations 4.8226737E-03 0.1455631 at 110iterations 2.4625086E-03 7.5775146E-02 at 120iterations finished qdiffx linear iterations at : 08:32:30 total time elapsed so far: 7.240000 # loops : 120 mean,max change (kT/e) : 2.4625086E-03 7.5775146E-02 energy calculations done at 7.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.470000 DelPhi exited at 08:32:31 7.470u 0.196s 0:08.16 93.8% 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 08:32:31 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 = 2081 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 3.239243 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): -20.75200 26.53600 ymin,ymax (A): -10.84000 26.15200 zmin,zma (A): -3.172000 46.28400 x,y,z range (A): 47.28800 36.99200 49.45600 scale (grids/A): 3.239243 object centre (A): 2.892001 7.656001 21.55600 number of atom coordinates read : 2081 total number of charged atoms : 1953 net assigned charge : 6.500009 assigned positive charge : 316.0039 centred at (gu) : 86.54707 86.48428 93.95425 assigned negative charge : -309.5042 centred at (gu) : 85.89191 86.57034 94.27483 start vw surface at 0.1900000 fill in re-entrant regions at 0.8500000 boundary points on vw surface= 178093 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17430 grid for indexing accessible points = 1.400000 m= 97735 mr = 132268 m= 40932 mr = 81836 m= 12084 mr = 33805 m= 2441 mr = 9424 m= 296 mr = 1786 m= 10 mr = 188 m= 0 mr = 0 time to grow re-entrant surface = 0.9300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.880000 number of dielectric boundary points 72284 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 15624 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) : 2.159495 object centre at (A) : 2.892001 7.656001 21.55600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3274364 0.7356733 midg,1,midg; midg,igrid,midg 0.3160633 4.5051770E-03 1,midg,midg; igrid,midg,midg 0.3988378 0.3388652 gauss-seidel spectral radius is 0.9993034 estimated iterations to convergence 299 setup time was (sec) 2.180000 now iterating at: 08:32:33 rms-change max change #iterations 10.51989 401.0696 at 10iterations 6.267836 125.6097 at 20iterations 3.722907 81.88180 at 30iterations 2.203562 40.14675 at 40iterations 1.300784 23.72934 at 50iterations 0.7683489 13.41383 at 60iterations 0.4522484 8.966838 at 70iterations 0.2667920 4.625610 at 80iterations 0.1565640 2.632568 at 90iterations 9.2266947E-02 1.532898 at 100iterations 5.4273546E-02 0.8846054 at 110iterations 3.1973310E-02 0.5861158 at 120iterations 1.8971190E-02 0.3235016 at 130iterations 1.1362717E-02 0.2042732 at 140iterations 6.9309729E-03 0.1373014 at 150iterations 4.3643685E-03 8.1245422E-02 at 160iterations 2.8736296E-03 5.1158905E-02 at 170iterations 2.0033750E-03 3.4263611E-02 at 180iterations finished qdiffx linear iterations at : 08:32:43 total time elapsed so far: 12.46000 # loops : 180 mean,max change (kT/e) : 2.0033750E-03 3.4263611E-02 energy calculations done at 12.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.67000 DelPhi exited at 08:32:44 12.673u 0.196s 0:13.17 97.6% 0+0k 0+0io 0pf+0w