On Thu, Jul 09, 2015, Michael Shokhen wrote:
>
> I am doing MD simulation at 310K by amber 14 of Michaelis complex (MC)
> of enzyme with peptide substrate applying the ff14sb force field and
> tip3p water in periodic box.
>
> Enzyme nucleophile like Ser or Cys can attack carbonyl carbon atom of
> substrate amide group from si- or re-site.
>
> The initial prochirality of the carbonyl carbon atom in the amide
> group of peptide substrate was of si-type. During 10 ns simulation the
> prochirality remains as si-type. Examining again the MC structure after
> 17 ns I have observed unexpected change of substrate prochirality from
> si to re.
>
> What is the reason of such abnormal structural isomerization of peptide
> amide group during amber MD simulation, and what commands should I
> add to the md.in script file in order to avoid irrelevant amide group
> isomerization?
I don't think there is any general answer to a question like this. You
presumably need to look at what happened between 10 and 17 ns to see the
nature of the transition that took place. You might then be able to decide if
this was indeed a problem, and see what artificial constraints might be used
to prevent it.
...dac
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Received on Mon Jul 13 2015 - 05:30:02 PDT
