VMD-L Mailing List

From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Sun Feb 08 2015 - 14:57:01 CST

I think your best option is to write each peptide to a PDB file and then just put them together using a text editor. As long as you give each peptide a different chain name VMD is very tolerant in this way - just copy-paste all the ATOM lines from one PDB file to the other (before the final END statement).

Cheers,

Tristan

________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Sourav Ray <souravray90_at_gmail.com>
Sent: Wednesday, 4 February 2015 9:25 PM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: Putting different peptide chains (spaced apart) in a single .xbgf file

Hello

With the help of Extensions -> Modeling -> Molefacture -> Start Molefacture -> Protein Builder -> Build. I can create a single peptide/protein chain of desired number of amino acids. However, I am not being able to insert multiple peptides in a single .xbgf file so that I can later save the coordinates as a .pdb file later. Actually I want to study peptide interaction. Kindly let me know if there is some way I can do that here or any alternative method that can be employed.

Thanks
Sourav