VMD-L Mailing List

From: Derman Baştürk (drmnbastrk_at_gmail.com)
Date: Tue Oct 11 2022 - 23:38:26 CDT

Dear NAMD Users,

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.

Best regards.

Derman