VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Fri May 04 2018 - 18:46:41 CDT

Hi Kelly,
Yes. Exclude them from the atomselection over which you are calculating the RMSD. Something like "protein and not (type NH3 CC OC or (type HC and withinbonds 1 of type NH3 and withinbonds 2 of name CA))" would work I think. The way to check would be to build up an atomselection that ONLY gives you the terminii, and then negate it to exclude it. VDW representations make this easier, since you can spot straightaway if you are catching something you don't want to be catching.
-Josh

On 2018-05-04 17:36:20-06:00 owner-vmd-l_at_ks.uiuc.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