Re: atom selection error

From: Vermaas, Joshua (
Date: Mon Dec 11 2017 - 11:28:09 CST

Yes. You don't even need to be adventurous! Its in the VMD user guide. You will notice that backbone, for instance, needs atoms with the name C, N, CA, and O, which are appropriate for atomic models. In a martini system, this selection will get you nothing.

On 12/11/2017 10:20 AM, Brian Radak wrote:

A lot of the shorthand selection syntax like "protein" "nucleic", "sidechain", and "backbone" are based on heuristics with the residue and atom names - an adventurous user could probably find these in the source code.

I would make your selection explicitly, since Martini probably breaks the heuristics.



On 12/11/2017 01:24 AM, Peter Freddolino wrote:
Do you still have backbone checked? The CG backbone beads don't count as backbone for vmd's atom selections...

On Mon, Dec 11, 2017 at 1:04 AM, Shahee Islam <<>> wrote:
thank you so much for your reply and i am really so sorry for my late reply.basically i have two same protein system.i made this system according to rbcg tutorial using martini force field.i am anlysing rmsd using vmd in built rmsd trajectory.first i upload psf and then the dcd.after this selecting backbone allign the system.then click rmsd.
the error is measure fit: no atoms selected.
the segname of my systems are ION,P1,P2,WT1,WT2.

when i made equvalent atom on and select atom BAS,still i have obtained the same erorr.

On Fri, Dec 8, 2017 at 11:24 PM, Peter Freddolino <<>> wrote:
Ok, so what atom selections are you using?

On Fri, Dec 8, 2017 at 9:22 AM, Shahee Islam <<>> wrote:
Thank you so much for your reply.i want to calculate the rmsd of backbone.And Still when I try to recentering the coarse grained proteins ,the atoms are not selecting.

On Dec 8, 2017 7:29 PM, "Peter Freddolino" <<>> wrote:
You would need to send much more information on how you're trying to calculate the RMSD. My wild guess is that you're looking for alpha carbon or recognizable backbone atoms when none exist.

On Fri, Dec 8, 2017 at 3:33 AM, Shahee Islam <<>> wrote:
i have prepared my system according to rbcg tutorial.Now i want to analyse my system by vmd,but during the analysis(rmsd) atoms are not selected and also in the time of recentering of proteins.Can anyone please help me why this is happening.
Also i want to know is there any other method to analyse the coarse grained system(which is made according to rbcg tutorial).

Thankig you
Shahee Islam
University of calcutta
Department of chemistry

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:20:45 CST