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

william Stebbeds willstebbeds at hotmail.com
Fri Feb 11 17:14:25 CET 2011

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
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