[gmx-developers] Strange default group behavior

[Jochen Hub]

Hi,

I noticed that, since gmx 4.5, some groups are twice in the default 
group selection. For example, I have a pdb file with residues SOL, HEX, 
SOQ and NA:

ATOM      1  C1  HEX     1      22.920  23.660  65.120  1.00  0.00 
      C
ATOM   5688  MW  SOL  1182       8.140   7.030   0.760  1.00  0.00
ATOM   5692  MW  SOQ  1183      21.970  25.660   4.180  1.00  0.00
ATOM   5693  NA  NA   1184      10.010   5.080   4.740  1.00  0.00


The default groups are:

   0 System              :     4 atoms
   1 Other               :     2 atoms
   2 HEX                 :     1 atoms
   3 SOQ                 :     1 atoms
   4 NA                  :     1 atoms
   5 Water               :     1 atoms
   6 SOL                 :     1 atoms
   7 non-Water           :     3 atoms
   8 Ion                 :     1 atoms
   9 HEX                 :     1 atoms
  10 SOQ                 :     1 atoms
  11 NA                  :     1 atoms
  12 Water_and_ions      :     2 atoms

The problem is now, that make_ndx and other tools throw an error if I 
try to select the group "HEX":

Error: Multiple groups 'HEX' selected

This is a very annoying behavior in scripts where different groups don't 
always have the same group number, so one wants so select a group by its 
name.

Btw, the problem disappears if one removes the "NA" line from the PDB 
file, which is even stranger.

Is this an intended behavior or should I file a redmine?

Many thanks,
Jochen


-- 
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Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189
http://cmb.bio.uni-goettingen.de/
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