VMD-L Mailing List

From: Josh (vermaasj_at_msu.edu)
Date: Mon Oct 23 2023 - 07:57:20 CDT

Hi Bill,

That previous post has most of it. The initial poster just couldn't have
the automatic first and last patches applied and still have it work.
Basically, a cyclic peptide is like any other, but at some point you end
up forcing a coupling that isn't what you'd expect for a linear polymer.
In CHARMM36, this weird topology can be described by the LINK patch if
you want to make a torus, or LIG1 if the loop is internal somewhere.

-Josh

On 10/22/23 6:38 PM, Bill McIntyre wrote:
> Hello everyone,
>
> Would someone please kindly provide me with some direction on how to
> make a script to build cyclic peptides in VMD from a provided list of
> sequences?  An output of PDB files for the sequences is sufficient
> (one separate PDB file per sequence).
>
> I saw there was a discussion in a previous mail posting that touched
> on this subject
> (https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2015-2016/0961.html
> <https://urldefense.com/v3/__https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2015-2016/0961.html__;!!HXCxUKc!21eBJ0NmTHVDf9x5FGwAWMQMsEXUNaYkk4A8z0VNGMsjc7iJZneLUbcDfyVNlxVMkQpd0xPOCp97QICEK0SHqB1WIoWC$>)
> but I didn't see any follow up that could guide me in doing this
> task.  Thanks.
>
> Bill McIntyre 

-- 
Josh Vermaas
vermaasj_at_msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
vermaaslab.github.io