normal Protein NH2 capping at C-end

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2 weeks 1 day ago #7716 by meicher
meicher created the topic: Protein NH2 capping at C-end
Dear Martini comunity,
I found on this forum for Martini 2.x that it is possible to use Nad bead instead of Qn for NH2 capping at proteins C-end. But in this new beta version I can't find such bead any more. So is there any other bead parametrised so far I can use or I just have to wait till this will be solved by Martini creators.
Thank you.

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1 week 3 days ago #7718 by bart
bart replied the topic: Protein NH2 capping at C-end
To me it is unclear what you want. I have a feeling you got confused with the bead types used for capping the charged residues of the N and C terminus of the complete protein, and the bead types used for certain elements of secondary structure (the beginning and end of a helix).

However, the backbone bead in Martini 3 varies depending on the attached aminoacid, we therefore do not make any distinction based on secondary structure.

If your question was, "what are the new capping bead types in their charged state at pH 7?", then it would become a Qp and Qn for the N and C side respectively.

Now the last option is if you meant the capping of a C-terminus with a amide group . in this case we would suggest using a P4. This is untested for now and a P5 could also work. Please let us know if this answered your question and share your results! :)

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1 week 3 days ago #7723 by meicher
meicher replied the topic: Protein NH2 capping at C-end
Thanks for the answer.
The past paragraph was what I needed - amide capping on C-terminus. I understand using Qp and Qn as I saw the results of converting scripts.
Sharing the results - of course, if I would have anything useful. :-)
Thanks again.

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