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
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