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

From: Eric H. Lee (ericlee_at_ks.uiuc.edu)
Date: Thu Jun 25 2009 - 11:16:16 CDT

Yes, it is built into Molefacture in VMD.

Eric H. Lee
Medical Scholars Program
Theoretical and Computational Biophysics Group, UIUC
ericlee_at_ks.uiuc.edu

On Jun 25, 2009, at 10:34 AM, 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

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