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
--
========================================
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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