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

[Justin Lemkul]

On 7/31/12 10:14 AM, Laura Kingsley wrote:
> 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?
>

Repeated groups are normal, but certainly undesirable. Since there is nothing 
functionally wrong with these groups, it's a rather low-priority bug and has 
been around since Gromacs 4.5 (so several years). The only way to prevent the 
duplicate groups would be to create an index file that eliminates the duplicates.

-Justin

>   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
>

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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