[gmx-users] Pulling Simulation Query

[Justin A. Lemkul]

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
> 

-- 
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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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