VMD-L Mailing List

From: Bassam Haddad (bhaddad_at_pdx.edu)
Date: Tue Jun 02 2020 - 11:44:55 CDT

Hi Yogesh,

You can use Hole <http://www.holeprogram.org/> to calculate the minimum
pore radii at each z-height, this will tell you where the constriction is,
and which amino acid is contributing to the minimum radii. You'll just have
to parse the hole outputs.

Best of luck,
Bassam

On Tue, Jun 2, 2020 at 4:41 AM Yogesh Sharma <yogesh.rma13_at_gmail.com> wrote:

> greetings everyone,
> hope you guys are doing good.
> I am interested in finding amino acids that are forming constrictions in
> protein pore throughout trajectory. I can do it manually for asingle frame
> but i am more interested in variations throughout trajectory in that
> region. can someone suggest the way ?
>
> *with regards*
> *Yogesh Sharma*
>
>