VMD-L Mailing List

From: Karl Decker (kaelenmitharos_at_gmail.com)
Date: Thu Jan 05 2017 - 14:46:29 CST

I asked one of my group members about it. Here's what he had to say:

"I usually use 3dna program, but curves+ is another option that I didn’t
try.

"To my best knowledge, neither 3dna nor curves+ is implemented to VMD as a
plugin. One can install 3dna (or curves+) program to their system, and
convert DCD to PDB, and use converted PDB as an input for those external
programs."

Thanks,
Karl

On Thu, Jan 5, 2017 at 7:33 AM, brataraj ghosh <bratarajghosh_at_gmail.com>
wrote:

> Dear VMD experts,
>
> I am attempting to analyze conformations of long dsDNA in various forms
> and base-pair compositions with simulations generated with NAMD.
>
> Is there a suitable plugin that can directly read DCD files and yield the
> DNA helical parameters, namely Roll, Tilt, Twist, Shift, Slide, Rise, as
> well as the Inclination angle?
>
> Your advice is appreciated.
>
> Thanks in advance,
> Brataraj Ghosh
>