[gmx-users] Intrinsically disordered proteins

[Justin A. Lemkul]

#ZHAO LINA# wrote:
> Hi,
> 
> 1. For those intrinsically disordered proteins, the sequence is known, 
> how the simulations will be set up, I mean, the first PDB will be 
> needed, how to get this one? (Ideally, not necessarily to be practical)
> 

http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources

> 2. suppose I got a PDB, there were several models there, let's say 16, 
> is it acceptable to just take one, say model 1?
> 

Making an arbitrary choice is not a good idea.  You have to justify that the 
model you selected is in some way representative of the ensemble.  You could do 
that by demonstrating that your simulation overlapped the configuration space of 
the ensemble in the PDB file, i.e. sampled all the expected configurations, thus 
the starting structure was not an inappropriate bias.

-Justin

> Thanks for any answering,
> 
> lina
> 

-- 
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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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