Hi,
I have used MacroMolecule Builder for similar things.
Erik
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.
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