[gmx-users] Re: Diagnosing + system blowing up

[Justin Lemkul]

On 7/31/12 7:46 PM, Shima Arasteh wrote:
>
>
>   But If I want to use acetyl instead of formyl, then what about the chemical activity of the formyl located in N-terminus?
> The protein that I will put in the bilayer is composed of 2 monomers . The monomers form a dimer from the N-terminus, the same as gramicidin A channel. Acetyl could be play the same role as formyl here?
>

If your reasoning for using a formyl group is for some functionally relevant 
information, then you need to do the hard work of parameterizing the molecule 
completely.  If you can substitute some other cap (like acetyl) then you have to 
justify it to a skeptical audience (reviewers).  The choice is yours alone.

-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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