[gmx-users] Amino Acids

[Justin Lemkul]

On 11/2/17 7:07 AM, rose rahmani wrote:
> Yes,sir ;)
>
> Termini?! nothing is mentioned about it!

Check again.

"The AAs considered in the simulations are endowed with the acetyl group 
at the N-terminus and N-methylamide group at the C-terminus. These caps 
eliminate the terminal charges and mimic the presence of a peptide chain 
in which the AA exists in the unionized form (see, e.g., Refs. 15 and 46)."

-Justin

>
> Sent from my iPhone
>
>> On Nov 1, 2017, at 11:39, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>>
>> Hi,
>>
>> Please try to keep to one email per question :-) Did you read the paper to
>> learn what termini they used?
>>
>> Mark
>>
>>> On Wed, 1 Nov 2017 07:34 rose rahmani <rose.rhmn93 at gmail.com> wrote:
>>>
>>> Hi
>>>
>>> If  standalone amino acids are zwitterionic and inappropriate for AMBER and
>>> GROMACS ,what do you think about this article?!
>>>
>>> Interactions of aqueous amino acids and proteins with the (110) surface of
>>> ZnS in molecular dynamics simulations
>>> *Article* in The Journal of Chemical Physics 140(9):095101 · March 2014
>>> DOI: 10.1063/1.4866763 · Source:PubMed
>>> <
>>> https://www.researchgate.net/publication/deref/http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpubmed%2F24606380
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
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