[gmx-users] Missing Amino Acids

[Justin A. Lemkul]

simon sham wrote:
> Hi,
> 1. I have a protein which is missing both the first and last amino acids 
> in the sequence. Do you know any free linux softwares that can insert 
> these missing amino acids?

A number of possibilities are listed here:

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

> 2. Since only two amino acids are missing, one in both end, can I simply 
> ignore them in simulations?
> 

If they're not functionally relevant or important to your aims, then probably. 
But no one on this list can answer that for you.

-Justin

> Thanks for your insight in advance.
> 
> Best,
> 
> Simon
> 
> 

-- 
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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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