VMD-L Mailing List

From: Miro Astore (miro.astore_at_gmail.com)
Date: Sat Oct 12 2019 - 17:14:12 CDT

You could use Avogadro, it's free.

On Sun., 13 Oct. 2019, 08:56 Mortimer Hemmit, <mortimer.hemmit_at_gmail.com>
wrote:

> 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
>