Dear Jason and Dac,
Thank you so much for the help. I came to a realisation that using the default charged terminii is the best for my system to be realistic.
Best regards,
Berin Karaman
Medicinal Chemistry
Institute of Pharmacy
Martin-Luther-Universität Halle-Wittenberg
Wolfgang-Langenbeck-Str. 4
06120 Halle (Saale), Germany
On Friday, 16 May 2014, 15:46, Jason Swails <jason.swails.gmail.com> wrote:
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 - 07:30:02 PDT
