[gmx-users] Need advice on appending aa residues to the sequence

Erik Marklund erikm at xray.bmc.uu.se
Wed Feb 13 09:49:19 CET 2013


I have used MacroMolecule Builder for similar things.


On Feb 13, 2013, at 4:41 AM, zugunder wrote:

> Hi,
> I am sorry if this topic is not relevant for GROMACS forum, but I hope
> someone has faced the same problem before and could give me some  
> advice...
> I need to simulate a relatively short protein (170aa) in water. No
> structures are available for it, so I used a Modeller web server to  
> get
> some. Unfortunately, they only provided me with several truncated  
> structures
> (with relatively high scores though) of 40 and 130aa length.  
> However, they
> do not overlap and the gap is 4aa long. While doing a research on  
> the better
> way to stitch them I ran a couple of simulations of 2 most high  
> scoring
> structures for a 130fragment (C-term) and one of them seems to fold
> relatively quickly.
> The problem now is that I can't find a way to append those 4  
> residues to
> either of the sequences and stitch them into one to simulate the  
> complete
> thing. I found several references to DeepView software, but it does  
> not seem
> to work in my hands (or probably I am missing something).
> So if someone has faced the same problem or has any ideas on how to  
> do this
> kind of reconstruction of the sequence for further simulation, I'd  
> really
> appreciate any tips, advice or other input.
> Thank you.
> --
> View this message in context: http://gromacs.5086.n6.nabble.com/Need-advice-on-appending-aa-residues-to-the-sequence-tp5005489.html
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