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Hi Folks,<br><br>I have added a custom DNA residue to the amber99sb ff, and everything works perfectly, (thanks to Justin!).<br><br>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.<br><br>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.<br><br>Is there a way of making gromacs understand that this residue is DNA when it makes the index files?<br><br>I am not using make_ndx, I just let gromacs split the groups.<br><br>Thanks in advance<br><br>Will - Cranfield University<br> </body>
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