[gmx-users] How to build a custom protein (PDB file)

[Justin A. Lemkul]

Quoting Ricardo Soares <rsoares at fcfrp.usp.br>:

> Hello everyone!
>
> I have a particular amino acid sequence and I wanna build a
> custom-shaped protein and make it a pdb file (I'm talking about
> non-realistic forms, like squares or a full extended chain). Can anyone
> indicate me some software for this task?

The xLeap module of Amber (now available freely as part of AmberTools) allows
you to draw a molecule of interest and do a basic energy minimization to
generate structures.

-Justin

>
> Thanx!
>
> --
> ___________________________________________________________
>
> Ricardo O. S. Soares
> Post-graduation Student in Biological Physics
> University of Sao Paulo - USP
> Faculty of Farmaceutical Sciences of Ribeirao Preto - FCFRP
> Phone: 55 (16) 3602-4840
> Curriculum Lattes - http://lattes.cnpq.br/0777038258459931
> ___________________________________________________________
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========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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