[gmx-users] (no subject)

RAHUL SURESH drrahulsuresh at gmail.com
Thu Jan 25 15:37:25 CET 2018

On Thu, Jan 25, 2018 at 7:43 PM, alex rayevsky <rayevsky85 at gmail.com> wrote:

> Dear users and developers!
> I have a question about replica exchange sampling and simulation annealing
> method. Well, I have a protein (TubulinG) X-ray, however it lack last 10-11
> residues, which are probably exposured to the solvent (and it seems are
> flexible enough to be invisible for X-ray). The protein exists in two
> isoforms, which differ on a single amino acid (approximately -15 position
> from the end), however, some in-house biochemical experiments stated that
> this change is crucial for motility of these terminal 10-15 residue.
> The problem is that I can't predict the exact initial location/conformation
> of the full-length C-termini and all standard MD simulations showed
> different, not similar, positions of the region - it can be either flexible
> or pinned to the 'protein's body' during the MD. It seems, that it depends
> on the seed which turns on a trigger for rotation of exposured straight
> 10-15 res. C-termini... Before starting a production MD for subsequent
> analysis I should be somehow ensured that the initial conformation is
> reliable. i-Tasser is not a good way, because it doesn't guarantee nothing,
> except the total minimization state, and homology modelling is also
> impotent.

Hi.. all the best. Start with errors is what I personally advice.
Rosetta fragment assembly method is one good approach or try contact
approach method. I believe they are good in defining protein structure.

Thank you

> That is why I want to start a preliminary MD to sample these C-terminal end
> (rebuild with any program like pymol, molsoft or swissmodel server) and I
> bet on these two approaches, mentioned above.
> Does anybody know is it possible, reasonable?
> where I can find a working tutorial to provide some changes or use it as it
> is?
> The additional question is about 'partial application' of the method to the
> fragment of the protein, to avoid time consuming calculations for the whole
> system, which is not a priority, as the final goal is just a minimized
> protein with a more informed preparation alghorithm.
> Thank You in advance!!!
> *Nemo me impune lacessit*
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*Rahul Suresh*
*Research Scholar*
*Bharathiar University*

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