From: Vermaas, Joshua (
Date: Wed Dec 19 2018 - 12:53:31 CST

Hi Prabir,

It isn't clear to me what you want to do, but I *think* you just want to simulate something akin to a cyclic peptide, right? Will you need to simulate the structure? If so, you'll need to become familiar with psfgen and the CHARMM force field. If not, what I've found to be the most straightforward is to just draw out the structure I want in Avogadro and use its minimization features to build the structure.


On 2018-12-18 21:34:43-07:00 wrote:

I want to prepare a ring-like hexamer from a monomer where two atoms of the
adjacent monomers will be restricted within a certain distance. Can anyone please suggest me how to do it using vmd?

Prabir Khatua
Postdoctoral Research Associate
Department of Chemistry & Biochemistry
University of Oklahoma
Norman, Oklahoma 73019
U. S. A.