[gmx-users] Orders of the residues in gromacs

[Mark Abraham]

On 3/02/2012 7:26 PM, Du Jiangfeng (BIOCH) wrote:
> Dear Justin and Jiangguo,
>
> It's still the issue about residue numbering. Actually, the gromacs version is 4.5.3, and I am using Martini coarse grained simulation, where I presume that gromacs reads residues from .gro file randomly, because there are no residues fetched correctly when I picked a list of residues for testing.
>
> Plus, I didn't use pdb2gmx program. In my gro file, it contains protein, lipids, ion, and water.
>
> :( :( :( :( :( :(

Residue numbering is not random - there's a rule that you don't 
understand, and that's quite a different thing :-) If you are interested 
in learning how to manage the rule, then there are better ways to 
approach your search for knowledge than to suggest that people providing 
you with free tools have gone out of their way to make their use 
frustrating! :-)

Mark