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

From: Amr Zeinalabideen Majul (
Date: Thu Jun 25 2009 - 10:34:43 CDT

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*.

Amr Majul

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