VMD-L Mailing List

From: Bill McIntyre (bill_mcintyre378_at_outlook.com)
Date: Tue Oct 24 2023 - 00:52:02 CDT

Hi Josh,

Thank you for clarifying that. Now the situation is that besides using the GUI for Molefacture to build a simple linear peptide, I have never built cyclic peptides (N to C connection) using VMD nor have I ever scripted building a peptide in VMD either.

Would you please advise me or direct me to where/who I can go to for building my cyclic (N to C connection) peptides? I have many of these to build so would you please point me to how I can build such cyclic peptides with a TKL script perhaps? I do not need to make psf files for them, just a series of simple pdb files for each sequence. Thanks.

Bill

________________________________
From: Josh <vermaasj_at_msu.edu>
Sent: Monday, October 23, 2023 7:57 AM
To: Bill McIntyre <bill_mcintyre378_at_outlook.com>; vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Script to Build Cyclic Peptides

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.htmld0xPOCp97QICEK0SHqB1WIoWC$>) 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<mailto:vermaasj_at_msu.edu>
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
vermaaslab.github.io