VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Fri May 04 2018 - 19:07:17 CDT

RMSD is usually calculated using a selection. By default the selection is
an entire molecule with keywords like "all" or "protein".

You can reduce your selection to start from residue 2 till N-1 -- or with
an even more complicated selection you can select Nter/Cter atoms.
The best way (in my opinion) is to use command-line options.

measure rmsd selection1 selection2

where selection1 and selection2 are your molecules excluding Nter/Cter.

Don't forget to eliminate any rotation/translation based components.

On Sat, May 5, 2018 at 10:47 AM, McGuire, Kelly <mcg05004_at_byui.edu> wrote:

> Is there a way to exclude the terminal patches (NTER and CTER) from the
> RMSD calculation?
>
>
> *Kelly L. McGuire*
>
> *PhD Scholar*
>
> *Department of Physiology and Developmental Biology*
>
> *Brigham Young University*
>
> *LSB 3050*
>
> *Provo, UT 84602*
>
>
> 

-- 
Best,
/A