How to set protonation states of certain atom in DNA with namd/vmd

From: raghav singh (
Date: Wed Mar 07 2012 - 07:15:55 CST

Hello All,

I am simulation DNA duplex but I want to make cytosine’s of one chain
protonated at N3 facing the center.
it would be great if someone provides me insights of the process or may be
how to patch nucleic acids so that it can be done.

it will a great help. I am stuck with since last couple of months.

Thank you


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