From: I. Camps (
Date: Thu Aug 29 2019 - 12:39:09 CDT

Dear all,

I am newbie using VMD.

My first task was to calculate the RMSD from a Molecular Dynamics done
using DESMOND.

I obtained the C-alpha and ligand RMSD using Maestro interface and using
the plug-in withing VMD.

The problem I am facing is that the results are different.

In the case of C-alpha, in both programs (Maestro and VMD), the selection
was: "backbone and name CA".
In the case of ligand, in Maestro it is just to select ligand. In VMD, the
ligand is identify as "UNK" residue.

Also, in both cases, the reference frame is the frame "0".

What I am doing wrong?


PS: I sent a previous email to this list with a figure attached. Does this
list accept attachments?