Natalie Stephenson wrote:
Hi ...
Just wondering if there's a way, during pulling simulations, to
immobilise say the C-terminus of the protein.
I've been running through the 'Umbrella Sampling' tutorial with my own
protein. Within this tutorial the ChainB is used as the immobile
reference - so it is this that is position restrained. Is there a way
of position restraining just one amino acid? How would I specify that in
the topology file?
Use genrestr with a custom index group to generate a posre.itp file for that
residue. Then, #include this new .itp file in your .top (just like what the
tutorial does).
-Justin
Thanks
Natalie
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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