[gmx-users] protein residue numbering not retained in GROMACS ?

Mark Abraham Mark.Abraham at anu.edu.au
Wed Nov 7 01:31:51 CET 2007

himanshu khandelia wrote:
> According to the documentation and the mailing lists, it seems that
> protein residue numbering is not retained in gromacs, is that correct
> ?
> No way to go around this ? There are, of course, obvious advantages of
> retaining residue numbers from pdb files.

No, there's no work-around. You could try renumbering by hand in the 
.top and final .gro structures, but I don't know if this works. In 
simple cases there's only a numerical offset for you to remember. If 
you're having to refer to literature references to residue 432 or such, 
then make yourself a lookup table and keep it handy.


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