unanswered How to cappe a C terminal residue in MARTINI? Is it important when the protein i

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1 year 2 months ago #7560 by z.sichaib

I am interested in simulating a Homology model of a Protein using MARTINI force field.

The model that I have is incomplete, I have four missing residues in the C terminal part.

So, my Cter residue in the model that I have is not supposed to be charged. I'm hesitating between neutralizing it or capping it (adding ACE group), I think the last one is the more appropriate.

In the other hand, I think that the capping residue (ACE ), is not included in martinize.py script.

Is there a way to 'martinize' it?
Have you any suggestions on how to do it?
For your experience, is ACE really needed or neutralizing the Cter residue is sufficient.

Thank you in advance for your help.

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