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-nt flag not producing expected result #487
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Termini parameters are defined as modifications (the link hacks you found are from a previous era ;) ). You can find them (for martini3001) in https://github.com/marrink-lab/vermouth-martinize/blob/master/vermouth/data/force_fields/martini3001/modifications.ff. The |
Thanks for the clarification, can see that now! |
I can see this might be related to #472, but I'm not 100% sure so am opening a separate issue.
From the aminoacids.ff file for martini, I would expect the following section regarding protein termini to make the N terminus (BB -BB) a P5 bead, and C terminus (BB +BB) a P6 bead:
However, if I run martinize2 with -nt, the result is that both BBs are of type P6.
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