VMD-L Mailing List

From: Mortimer Hemmit (mortimer.hemmit_at_gmail.com)
Date: Sat Oct 12 2019 - 16:31:04 CDT

Hello,

I am trying to create a small peptide with the Molefacture Protein Builder
in VMD 1.9.3. However, the first residue hangs off at an odd angle and the
resulting structure is not straight.

To reproduce:

Open VMD 1.9.3
Open Extensions -> Modeling -> Molefacture
Click "Start Molefacture"
Open Build -> Protein Builder
Click "Straight"
Type in the peptide codes (for me, it is deca-alanine "AAAAAAAAAA". Using a
larger amino acid such as lysine makes it more apparent.)
Click "Build"
Click "Yes"

One of the amino acids is bent. How may I create a completely straight
peptide?

Any help would be greatly appreciated,
Mortimer