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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