Re: minimization with symmetry restrain

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Dec 13 2013 - 16:48:32 CST

The symmetry restraints will work fine independent of MDFF. The tutorial for MDFF (I think) and the user guide are the only places its described though.

On Dec 13, 2013, at 1:31 PM, flavio seixas <oivalf_nix_at_yahoo.com> wrote:

> Hi,
> I modeled an homotetrameric protein with Modeller software, using symmetry restrains aplyed to all Ca atoms. Chains B, C and D are symmetrical to A chain.
> Now I want to minimize the pdb model using NAMD2 CG method and the same symmetry restrain.
> I was looking NAMD user guide and Namd-list for similar topics and the only reference I found regards MDFF method.
> My questions are:
> 1) Is it also posible to aply symmetry on CG minimizing using NAMD?
> 2) Is there a tutorial, script or reference to guide me?
>
> regards,
>
> Flavio
>
> -------------------------------------
> Flavio Augusto Vicente Seixas
> Laboratory of Structural Biochemistry
> Department of Biochemistry
> Universidade Estadual de Maring, PR, Brazil
> http://www.uem.br

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