VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Tue Apr 28 2020 - 04:57:54 CDT

To select DNA use

nucleic

See documentation :

https://www.ks.uiuc.edu/Research/vmd/vmd-1.3/ug/node132.html

On Tue, 28 Apr 2020, 4:42 PM Seojin You, <seojinyou64_at_gmail.com> wrote:

> Hello,
> I am struggling to draw RMSD plots from a dcd file containing DNA and
> water.
> I am using RMSD Trajectory Tool on VMD, and it has "protein" as default
> for atom selection.
> I cannot find the correct keyword to select DNA molecule instead of
> protein.
> So my questions are: Is DNA an accepted term here? And if so, what keyword
> should I use to select it? Or does VMD analysis only work for proteins?
> I would appreciate any help I can get on the analysis tools for DNA.
> Thank you in advance.
>