[gmx-users] make_ndx: duplicates groups appearing in index.ndx file

[Laura Kingsley]

Hello,

I've just switched from using Gromacs version 4.0.5 to 4.5.5, and I'm 
having an issue with make_ndx. Using the old version I have a single 
group showing up for each "odd" residue, eg JJJ shows up once as group 
16 for example. When I use the new version on the same file I get 2 
groups appearing for residue JJJ and others. Here is the output of that 
I get from make_ndx. Is there some way I can prevent this?

  0 System              : 126928 atoms
   1 Other               :   137 atoms
   2 NGL                 :     9 atoms
   3 CY1                 :    10 atoms
   4 CAR                 :    25 atoms
   5 HEM                 :    73 atoms
   6 JJJ                 :     1 atoms
   7 CPZ                 :    19 atoms
   8 Cl                  :     6 atoms
   9 Protein             :  7475 atoms
  10 Protein-H           :  3733 atoms
  11 C-alpha             :   461 atoms
  12 Backbone            :  1383 atoms
  13 MainChain           :  1844 atoms
  14 MainChain+Cb        :  2275 atoms
  15 MainChain+H         :  2275 atoms
  16 SideChain           :  5200 atoms
  17 SideChain-H         :  1889 atoms
  18 Prot-Masses         :  7475 atoms
  19 non-Protein         : 119453 atoms
  20 Water               : 119310 atoms
  21 SOL                 : 119310 atoms
  22 non-Water           :  7618 atoms
  23 Ion                 :     6 atoms
  24 NGL                 :     9 atoms
  25 CY1                 :    10 atoms
  26 CAR                 :    25 atoms
  27 HEM                 :    73 atoms
  28 JJJ                 :     1 atoms
  29 CPZ                 :    19 atoms
  30 Cl                  :     6 atoms
  31 Water_and_ions      : 119316 atoms


Thanks,

- Laura

-- 
Laura Kingsley

Graduate Student
Medicinal Chemistry and Molecular Pharmacology
Purdue University
Office: RHPH 504A
575 Stadium Mall Dr.
West Lafayette, IN 47907
Office Phone: (765) 496-6643