<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">If I do just the commands you provided below on the models you attached earlier 1a30_protein/ligand, I do not get the no-GAFF error you got. I get a different (and later) error that is going to be problematic. Add Ions does not work on multiple models in aggregate — if given multiple models it will add ions to each separately, which is an issue since you’ve separated your receptor and ligand into different models. If you add ions to just the receptor, it could very well place one in the ligand binding pocket. If you combine your ligand and receptor into a single model, that could work but would be more complicated and will probably be a headache. :-(<div class=""><br class=""></div><div class="">Anyway, I’ve attached the script I used that did not get the GAFF error so you can try it yourself on the 1a30 system. You could let me know what additional factors are needed to get the no-GAFF error, assuming that the other Add Ions issue isn’t a showstopper.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""></div><div class=""></div></body></html>