[gmx-users] Programs to add residues

[Michael Lerner]

On Tue, Jun 21, 2011 at 4:12 PM, Chris Neale <chris.neale at utoronto.ca>wrote:

> Try "Loopy". You can get it to build termini in addition to loops.
>
> http://wiki.c2b2.columbia.edu/**honiglab_public/index.php/**Software:Loopy<http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Loopy>
>
>
I've also seen people use PyMOL's builder to do this. Either way, you'll
need to take (a lot of) extra care to minimize your linker and make sure
that it looks reasonable.

-Michael


> Nevertheless, I'd suggest simply omitting that part of the protein and
> capping your new terminus to remove the charge. You will have more
> difficulties converging the conformation of the unstructured terminus than
> you may expect.


> CHris.
>
> -- original message --
>
> Hi all,
>
> Is there a program that allows the user to add residues to the N and C
> terminus, without using the electron density?  I would like to add a
> short linker to my protein which doesn't exist in the electron
> density.
>
> Thanks a lot,
>
> Sincerely,
> Zack
>
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-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
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