On May 16, 2014, at 8:39 AM, berin karaman <berinkaraman.yahoo.com> wrote:
> Dear Dac.
>
> Thank you very much for the clarification.
>
> I was just wondering since the residues would be charged then wouldn't it effect the binding of the peptide to the protein in that specific points through the simulation ?
>
> Do you think putting protecting groups to the N and C terminal (ACE and NME) instead of using charged amino acid residues gives more realistic results ?
These are completely different systems! If you want to model a compound with neutral capping groups, the neutral capping groups will give more "realistic" results. Otherwise, use the charged termini for more "realistic" results.
What you should do depends entirely on what you want to model and what you want to learn. To the best of your ability, your simulation should reflect experiment as closely as possible.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri May 16 2014 - 07:00:03 PDT
