[gmx-users] (no subject)

alex rayevsky rayevsky85 at gmail.com
Thu Jan 25 15:14:25 CET 2018

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

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
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*

More information about the gromacs.org_gmx-users mailing list