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marrink-lab / vermouth-martinize

Describe and apply transformation on molecular structures and topologies
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-nt flag not producing expected result #487

Closed csbrasnett closed 1 year ago

csbrasnett commented 1 year ago

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:

[ link ]
[ molmeta ]
neutral_termini true
[ atoms ]
BB {"replace": {"atype": "P5"}}
[ non-edges ]
BB -BB

[ link ]
[ molmeta ]
neutral_termini true
[ features ]
neutral_termini
[ atoms ]
BB {"replace": {"atype": "P6"}}
[ non-edges ]
BB +BB

However, if I run martinize2 with -nt, the result is that both BBs are of type P6.

pckroon commented 1 year ago

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 -nt flag is hardcoded to apply the modifications 'COOH-ter' and 'NH2-ter' (https://github.com/marrink-lab/vermouth-martinize/blob/master/bin/martinize2#L606). Make sure you're running a version of martinize in which #476 and #477 have been merged.

csbrasnett commented 1 year ago

Thanks for the clarification, can see that now!