[gmx-users] renumbering residue numbers for version 4.0.2

[Mark Abraham]

On Fri, Mar 29, 2013 at 2:10 PM, Nash, Anthony
<Anthony.Nash at warwick.ac.uk>wrote:

> Apologies if this has been covered once before, I've had a hearty search
> and I've yet to find anything.
>
> I have just installed a modified verison of Gromacs 4.0.2 which calculate
> lateral pressure. However, when I run grommp I get:
>
> Residue numbers in the .top are not numbered consecutively from 1 (rather,
> resnumber = 652 and resnr_diff = -1)
>
> Yet, running grompp on the same files with version 4.5.1 everything is
> perfectly fine. I am guessing somewhere in between the two versions
> something was changed.
>
> So, does this sound about right? Does the order of residue numbers no
> longer mater with the latest versions of grompp? And ultimately, does
> anyone know how I can go through a .gro file and renumber every residue
> (short of writing a perl script)?
>

Use genconf -renumber from probably any version (and curse whoever thought
that was a good place to put it :-))

Mark