[gmx-users] Re: combine mutiple PBDs

[Justin Lemkul]

On 3/29/13 7:16 AM, zalikha_ibrahim wrote:
> Thanks f your reply, Dr.
>
> I wanted to do PCA analysis on this x-ray structures compilation. Does that
> mean I need to pretreat (i.e. fixing missing residues) those PDBs before
> compiling it?
>

Yes, or otherwise analyze a subset of atoms that corresponds to some common 
portion of all the proteins.  If you insert missing residues, then they have 
artificial positions; this may flaw your analysis.  Actual simulations may be 
better than just hacking together a bunch of incomplete X-ray structures.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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