When should I use NTER and NNEU as a patch?

From: Derman Basturk (drmnbastrk_at_gmail.com)
Date: Wed Oct 12 2022 - 12:46:17 CDT

Dear NAMD Users,

I previously posted this question in VMD mailing list but it is actually
more related to the NAMD mailing list. I would appreciate any input.

My understanding is that when I have a full-length protein structure then I
should use NTER and CTER as patches in the N and C terminus, except special
cases when you have proline or glycine at the terminals. But what should I
use if I do not have a full-length protein? Should I use the regular NTER
or the neutral NNEU? I am asking because if I use NTER, I would be placing
a positive charge at a location that would normally not be there. I
couldn't find any detailed info on this. Any suggestion or reading material
on this would be appreciated.



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