[gmx-users] Add custom residue to DNA index group

Mark Abraham Mark.Abraham at anu.edu.au
Fri Feb 11 17:33:15 CET 2011

On 12/02/2011 3:14 AM, william Stebbeds wrote:
> Hi Folks,
> I have added a custom DNA residue to the amber99sb ff, and everything 
> works perfectly, (thanks to Justin!).
> The residue is incorporated perfectly into the sequence, with no 
> abnormal events during simulations. I have updated all the files to 
> include the new residue.
> I have since realised, when using g_rms, that my custom residue is not 
> included in the default DNA index group, and appears as a group on its 
> own.
> Is  there a way of making gromacs understand that this residue is DNA 
> when it makes the index files?
> I am not using make_ndx, I just let gromacs split the groups.
> Thanks in advance
> Will - Cranfield University

You need to arrange for the tools to access a modified form of 
share/gromacs/top/residuetypes.dat with your custom residue suitably 
classified. I understand you can copy that file to your working 
directory and modify it there, and GROMACS will use the local copy.

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