[gmx-users] Simulating Peptides

su sun.iba2 at gmail.com
Wed Jul 8 17:59:11 CEST 2015

Thank You very much for the quick and detailed reply. I will study more according to points you mentioned and then start any fruitful simulation.
Best Regards

Sent from my iPhone

> On 08-Jul-2015, at 7:31 pm, Mateusz Marianski <marianski at fhi-berlin.mpg.de> wrote:
> Hi Suniba,
> You touch here very complicated system that requires lot of literature research first. Few hints:
> 1. Amyloid-Beta (AB) is intrinsically disordered protein. The PDB you point to is a nmr structure measured in some helix-inducing solvent and it does not maintain the structure in water (physiological) solution. Thus I would be reluctant to study its "unfolding" because it might bring little of relevance to the water solution. If You want to look at the AB free-energy landscape in water, I would suggest looking at Pande's paper first: doi:10.1016/j.bpj.2011.12.002
> 2. Following from the paper, in water You face all sort of sampling problems, thus You need to reach really long time scales to obtain any meaningful result. Otherwise You might be biased toward some metastable states which stability are just artifacts of poor sampling/short timescales.
> 3. There's no full AB plaques structure (as far as I am aware), just its hydrophobic part (vide PDB 2beg (mono), 2lmn (di) and 2lmp (tri)). You will probably find some refs in under this pdb's.
> Best,
> Mateusz
>> On 07/08/2015 03:35 PM, su wrote:
>> Hello
>> I am going to simulate the Unfolding process of Amyloid beta peptide (PDB ID 1IYT) and the fibrillar structure as well, Alone and with ligands. Can anyone suggest a good tutorial or reference article for the same? For the papers that i studies, none has explained the MD process.
>> Regards
>> Suniba
>> Sent from my iPhone
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> Mateusz Marianski, PhD
> email:          marianski at fhi-berlin.mpg.de
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