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

zugunder schlecht at mail.ru
Wed Feb 13 04:41:08 CET 2013


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.

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