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.