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
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