Re: Does NAMD have any capability to assign coordiantes to novel sequences?

From: Nicholas M Glykos (glykos_at_mbg.duth.gr)
Date: Thu Jun 25 2009 - 11:36:02 CDT

'Ribosome' at http://www.roselab.jhu.edu/~raj/Manuals/ribosome.html should
do the trick.

Nicholas

On Thu, 25 Jun 2009, Amr Zeinalabideen Majul wrote:

> Hello all,
>
> Been working through most of the tutorials, especially the one about
> Parameterizing Novel resides, but I was wondering where would I get a
> PDB file for a completely novel sequence. Working with relatively small
> sequences of 10-20 amino acids, if I randomly pick amino acid sequences,
> can NAMD generate a pdb file for a sequence with randomly picked
> coordiantes? Or are there any structural viewing programs that can do
> that? One with a command line or one that I can run off a script so that
> I can generate PDB files for hundreds of sequences stored in a text file
> *Fasta format for example*.
>
> Thanks
> Amr Majul
>

-- 
          Dr Nicholas M. Glykos, Department of Molecular Biology
     and Genetics, Democritus University of Thrace, University Campus,
  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
    Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/

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