From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Fri Aug 06 2010 - 02:40:35 CDT

Hi,

you could probably use the
molfacture<http://www.ks.uiuc.edu/Research/vmd/plugins/molefacture/>plugin
(and it's protein builder) to generate such a peptide.

Best regards,
Ajasja

On Thu, Aug 5, 2010 at 21:24, Gregorio Alanislobato <
gregorio.alanislobato_at_kaust.edu.sa> wrote:

> Hi,
>
> Say that I have a protein whose amino acid sequence is ABCD and I want to
> insert Asparagines between B and C (4) and to the end (2), so that I will
> end up with a protein with sequence AB*NNNN*CD*NN. *Is there any easy way
> I can do this in VMD? What I have is a PDB file with half of the protein
> folded (which would be AB) and the other half denatured (CD). I'm ran a
> simulation without insertions and the protein folded just as I wanted, now I
> want to run a simulations with the insertions (Asparagines runs) and I'm
> expecting a diferent folding.
>
> Regards,
> --
> Gregorio Alans Lobato, BSc
> 4700 KAUST Mail Box: 1899
> Thuwal 239556900, KSA
> Student ID: 100037943
> Badge #: 101969
> Mobile Phone: +966-564-75-14-14
> e-mail: gregorio.alanislobato_at_kaust.edu.sa