Sat Oct 8 14:23:51 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 14:23:51 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3024 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 0.6412681 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): -12.26300 43.25200 ymin,ymax (A): -22.26900 22.52100 zmin,zma (A): -7.499000 46.85300 x,y,z range (A): 55.51500 44.79000 54.35200 scale (grids/A): 0.6412681 object centre (A): 15.49450 0.1259995 19.67700 number of atom coordinates read : 3024 total number of charged atoms : 2877 net assigned charge : -0.9999929 assigned positive charge : 452.5116 centred at (gu) : 88.78680 89.55531 91.70866 assigned negative charge : -453.5123 centred at (gu) : 88.75178 89.46001 91.65528 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8219 nv = 96 ne = 84 npr = 63537 no. pairs analyzed = 63537 no. exposed pairs = 3420 no. arc points = 23980 no. surface atoms = 1158 nbur = 1866 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 421 mr = 4805 m= 1 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3792 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2314 ## 222 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 10008 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.2757581E-09 8.7105088E-09 midg,1,midg; midg,igrid,midg -1.6549928E-08 1.0652338E-08 1,midg,midg; igrid,midg,midg -8.3775102E-09 2.5959606E-09 gauss-seidel spectral radius is 0.9874317 estimated iterations to convergence 73 setup time was (sec) 0.6700000 now iterating at: 14:23:52 rms-change max change #iterations 0.1606476 22.88433 at 10iterations 1.6488614E-02 2.252000 at 20iterations 1.6884055E-03 0.2519684 at 30iterations 1.9549532E-04 2.8289795E-02 at 40iterations 2.6907022E-05 3.7803650E-03 at 50iterations finished qdiffx linear iterations at : 14:23:55 total time elapsed so far: 4.370000 # loops : 50 mean,max change (kT/e) : 2.6907022E-05 3.7803650E-03 energy calculations done at 4.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.540000 DelPhi exited at 14:23:56 4.549u 0.397s 0:05.25 93.9% 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 Sat Oct 8 2011 at 14:23:56 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3024 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 1.923804 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): -12.26300 43.25200 ymin,ymax (A): -22.26900 22.52100 zmin,zma (A): -7.499000 46.85300 x,y,z range (A): 55.51500 44.79000 54.35200 scale (grids/A): 1.923804 object centre (A): 15.49450 0.1259995 19.67700 number of atom coordinates read : 3024 total number of charged atoms : 2877 net assigned charge : -0.9999929 assigned positive charge : 452.5116 centred at (gu) : 86.35979 88.66562 95.12507 assigned negative charge : -453.5123 centred at (gu) : 86.25519 88.37971 94.96542 start vw surface at 0.1300000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 89756 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23980 grid for indexing accessible points = 1.400000 m= 32179 mr = 64873 m= 4695 mr = 24110 m= 281 mr = 2842 m= 10 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 393 time to turn everything in is 0.7100000 number of dielectric boundary points 34992 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 151 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 22631 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) : 0.6412681 object centre at (A) : 15.49450 0.1259995 19.67700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7263966E-02 9.2638163E-03 midg,1,midg; midg,igrid,midg -1.8976888E-03 2.1764165E-02 1,midg,midg; igrid,midg,midg -4.2341184E-02 5.8574807E-03 gauss-seidel spectral radius is 0.9986946 estimated iterations to convergence 219 setup time was (sec) 1.010000 now iterating at: 14:23:57 rms-change max change #iterations 4.720002 219.9436 at 10iterations 2.263229 75.59827 at 20iterations 1.077224 34.90882 at 30iterations 0.5134975 16.99537 at 40iterations 0.2456408 6.691292 at 50iterations 0.1169467 3.200767 at 60iterations 5.5822961E-02 1.666770 at 70iterations 2.6703438E-02 0.7767029 at 80iterations 1.2779867E-02 0.3546906 at 90iterations 6.0918112E-03 0.1668556 at 100iterations 2.9060594E-03 8.6997986E-02 at 110iterations 1.3902416E-03 3.8124084E-02 at 120iterations finished qdiffx linear iterations at : 14:24:07 total time elapsed so far: 10.54000 # loops : 120 mean,max change (kT/e) : 1.3902416E-03 3.8124084E-02 energy calculations done at 10.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.71000 DelPhi exited at 14:24:07 10.714u 0.441s 0:11.50 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 Sat Oct 8 2011 at 14:24:07 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3024 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 2.885706 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): -12.26300 43.25200 ymin,ymax (A): -22.26900 22.52100 zmin,zma (A): -7.499000 46.85300 x,y,z range (A): 55.51500 44.79000 54.35200 scale (grids/A): 2.885706 object centre (A): 15.49450 0.1259995 19.67700 number of atom coordinates read : 3024 total number of charged atoms : 2877 net assigned charge : -0.9999929 assigned positive charge : 452.5116 centred at (gu) : 84.53955 87.99828 97.68752 assigned negative charge : -453.5123 centred at (gu) : 84.38265 87.56955 97.44819 start vw surface at 0.1300000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 207708 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23980 grid for indexing accessible points = 1.400000 m= 106161 mr = 156526 m= 36933 mr = 88313 m= 8362 mr = 29621 m= 1153 mr = 6141 m= 65 mr = 722 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 1373 time to turn everything in is 1.860000 number of dielectric boundary points 79024 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.080000 number of grid points assigned charge 23011 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) : 1.923804 object centre at (A) : 15.49450 0.1259995 19.67700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.1968488E-02 0.2862469 midg,1,midg; midg,igrid,midg 3.9929147E-03 0.2450107 1,midg,midg; igrid,midg,midg -0.5890675 0.1497242 gauss-seidel spectral radius is 0.9992774 estimated iterations to convergence 294 setup time was (sec) 2.280000 now iterating at: 14:24:10 rms-change max change #iterations 10.96777 451.7371 at 10iterations 6.429879 143.9168 at 20iterations 3.738228 67.91151 at 30iterations 2.180058 40.29433 at 40iterations 1.262593 20.55632 at 50iterations 0.7346610 14.29590 at 60iterations 0.4256790 7.354111 at 70iterations 0.2463337 4.027351 at 80iterations 0.1431389 2.414932 at 90iterations 8.2779296E-02 1.337159 at 100iterations 4.7844574E-02 0.7803688 at 110iterations 2.7669800E-02 0.4284229 at 120iterations 1.6054118E-02 0.2753601 at 130iterations 9.2916870E-03 0.1479673 at 140iterations 5.3940811E-03 8.4571838E-02 at 150iterations 3.1248869E-03 5.2227020E-02 at 160iterations 1.8169472E-03 2.8608322E-02 at 170iterations 1.0580927E-03 1.6630888E-02 at 180iterations finished qdiffx linear iterations at : 14:24:26 total time elapsed so far: 18.34000 # loops : 180 mean,max change (kT/e) : 1.0580927E-03 1.6630888E-02 energy calculations done at 18.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.52000 DelPhi exited at 14:24:27 18.524u 0.472s 0:19.26 98.5% 0+0k 0+0io 0pf+0w