From: John Stone (
Date: Wed Nov 13 2019 - 00:38:47 CST

What simulation tool is producing the series of PDB files you're
working with? Can you use the "dynamic bonds" representation for
visualization purposes, or are you doing quantitative analysis
based on the existence of these bonds?

  John Stone

On Sat, Nov 02, 2019 at 09:13:18AM +0330, Hoda Shirzad wrote:
> Hello,
> I am generating PDB files during my MD simulations which¬ contain bond
> information via "connect" order. The bonds are updating during the
> simulation, but VMD does not update the bonds.¬
> How can I visualize the updated bonds?
> I found [1]this link in¬ my searches, However, It is an old program and
> cannot be used.¬
> Thank you,
> Hoda
> References
> Visible links
> 1.

NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801           Phone: 217-244-3349