Fwd: Re: Bactenecine

From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Wed Mar 16 2011 - 16:35:57 CDT

Andres,

Along with VMD, you could try with VegaZZ
(http://nova.colombo58.unimi.it/cms/index.php?Software_projects:VEGA_ZZ:Download),
free software. There you will find user-friendly peptide builder. Also,
program is very suitable for setting-up NAMD calculations, as well as
for trajectory analysis. Other way is to sketch peptide in 2D and
convert it to 3D by, for example, CORINA (on-line free), see
http://www.molecular-networks.com/online_demos/corina_demo , also
openeye (http://www.eyesopen.com/omega) offer great program for SMILES
to 3D conversion OMEGA (free for academia)

Branko

On 3/16/2011 8:22 PM, Andres Morales N 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/
> <http://www.ciencias.epn.edu.ec/%7Ebiomod/>
>
>
>
>
>
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