Re: Bactenecine

From: johan strumpfer (johanstr_at_ks.uiuc.edu)
Date: Wed Mar 16 2011 - 15:54:46 CDT

Hi Andres,

You could try the molefacture plugin part of VMD. It has a protein
builder function that will give you a starting structure.

Cheers,
Johan

On Wed, Mar 16, 2011 at 3:22 PM, Andres Morales N
<andresmoralesn2_at_hotmail.com> wrote:
>
> Hi!
>
> I know the sequence of the peptide. The main problem is that I don't know
> how to built it. Coul I do it with VMD or any other program?
>
> Kind regards
>
>
> Andres
>
>
>
>
>
> ________________________________
> Date: Wed, 16 Mar 2011 08:54:00 -0700
> From: rwoodphd_at_yahoo.com
> Subject: Re: namd-l: Bactenecine
> To: andresmoralesn2_at_hotmail.com
>
> Do you know the sequence of this peptide?  If so, couldn't you build it and
> then "dock" it into your membrane (or a piece of it)?  That's how I placed a
> molecule on the surface of a membrane.
>
> Richard
>
>
> ________________________________
> From: Andres Morales N <andresmoralesn2_at_hotmail.com>
> To: VMD <vmd-l_at_ks.uiuc.edu>; NAMD <namd-l_at_ks.uiuc.edu>
> Sent: Mon, March 14, 2011 11:11:05 PM
> Subject: namd-l: Bactenecine
>
> Dear Users:
>
>
>
> I need to simulate the interaction of the peptide (Bactenecine) with a
> phospholipid monolayer. So I haven’t be able to find Bactenecin’s crystal
> structure (pdb file) yet. Does anybody know where I could find it?  Another
> option is to model that peptide since its amino-acid sequence, i.e, I need
> to make a pdb file of its random coil using special coordinates of its atoms
> (it is a 19-reside peptide). I haven’t worked in this before. Could I use
> VMD to do it? Or is there any program to do it?  I hope anybody can help me.
>
>
>
> Kind regards
>
>
>
>
>
>
>
>
>
>
>
>
>
> Andrés Morales N.
> Biophysics and Molecular Modelling Group
> Physics Department
> Escuela Politecnica Nacional, Quito-Ecuador
> Ladron de Guevara E11-253.
> Phone: 593-95292408
> http://www.ciencias.epn.edu.ec/~biomod/
>
>
>
>

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