Tutorial-l Mailing List

From: SHIVAM TIWARI (t.shivam_at_iitg.ac.in)
Date: Thu Jan 28 2021 - 10:38:22 CST

Thanks for the reply

regards
shivam
________________________________
From: Gumbart, JC <gumbart_at_physics.gatech.edu>
Sent: Thursday, January 28, 2021 9:46 PM
To: SHIVAM TIWARI <t.shivam_at_iitg.ac.in>
Cc: tutorial-l_at_ks.uiuc.edu <tutorial-l_at_ks.uiuc.edu>
Subject: Re: tutorial-l: rules for grouping atoms

Hi Shivam,

Sorry for the delayed reply; I think not many people monitor the tutorial mailing list.

My understanding is that the original idea behind groups was that they would have integer charge, so essentially anything strongly interacting would be put together. However, in practice, it’s not relevant as at least in VMD/NAMD, the GROUP label in the topology file isn’t used.

Best,
JC

On Jan 28, 2021, at 10:13 AM, SHIVAM TIWARI <t.shivam_at_iitg.ac.in<mailto:t.shivam_at_iitg.ac.in>> wrote:

Dear all,
This is regarding the topology tutorial. A particular line in the tutorial under the section for Glutathione topology creation is like this "In the original glutamic acid residue, the side chain is quite electronegative, and draws electron density from the CH2 atoms next to it, so the entire set C2 H2 O2 is a single GROUP. In ã-Glu, however, since the “side chain” more resembles a peptide bond, we separate it into three GROUPs: CH2 , CH2 , and CO." So I was wondering if anyone can elaborate on the rules for creating a group, that is, how exactly to decide on grouping the atoms. Are there any standard rules for it?

regards
shivam

**
** Visit http://www.greatcircle.com/majordomo/ for more info on majordomo
**