normal Capping residues

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2 years 1 month ago #7243 by edesantis
Capping residues was created by edesantis
Hallo MARTINI FORUM,

I am an italian PhD student.
I am intresting in a simulation of a system composed of amyloid proteins and smaller compounds, named beta-sheet-breaker that are able to alterate amyloid aggregation process.
these small peptides, in the all atomistic model, are provided with capping residues (named ACE and NH2), these residues are not included in martinize.py script,
is there a way to martinaze them?
have you any suggestion to do it?
for your experience are them really needed?

thanks in advance
Emiliano

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1 year 2 months ago #7559 by z.sichaib
Replied by z.sichaib on topic Capping residues
Hi Emiliano,

I'm asking the same questions about the CAP termini.

My problem is that I have an incomplete protein model so the C terminal part is not supposed to be charged. I was thinking that if I simply neutralize it, it wouldn't be very correct. I prefer capping it so it will be more 'correct' and 'clean'.

Since you had this problem before, can I have your feedback about this, please? Did you arrange to cap your protein?

Thank you in advance for your help.

Best.

Zeineb

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