[gmx-users] Loop refirement using simulated annealing

[James Starlight]

Hi Chris,

Many thanks for suggestions! This time I'd like to refine only loops (10-15
residues) of my models. I've tried to use SA refirement implemented in the
Modeller (which is resemble mostly monte-carlo SA) but always obtained
not-native like results (for instance elements of secondary structures seen
in X-ray structures of these proteins have been always absent after such
refinement. In this regsaards such refined loops have been looks mostly
like random coils.  In this case I'd like to test some force-field based SA
with the inclusion of implicit solvent models.

James


2014-05-28 0:21 GMT+04:00 Christopher Neale <chris.neale at alum.utoronto.ca>:

> If you are just looking for reasonable loop conformation, you could also
> use:
> modeller -- https://salilab.org/modeller/
> loopy --
> http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Loopy
>
> If you want to fold the loop, then I am not sure SA will be sufficient in
> the absence of any experimental restraints. I might be able to help more if
> you provide information about what you want to obtain and how long your
> loops are. If you simply want to use gromacs to turn a terrible initial
> conformation into a plausible disordered loop conformation, then I am not
> sure that your exact protocol matters too much. If you want reliable
> ensembles (given the force field), then I would suggest replica exchange
> with restraints as you mentioned. This could likely be done much more
> efficiently using replica exchange with solute tempering and only temper
> the loops (not sure if that is in gromacs 5 though, it is not in 4.6.x as
> far as I know).
>
> As with any high-temperature simulations or simulations starting from
> drastically poor conformations, be careful to analyse for chiral inversions
> and cis backbone omega angles.
>
> Chris.
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of James
> Starlight <jmsstarlight at gmail.com>
> Sent: 27 May 2014 16:11
> To: Discussion list for GROMACS users
> Subject: [gmx-users] Loop refirement using simulated annealing
>
> Dear Gromacs users!
>
>
> I need to refine some flexible regions (mainly long loop and linker
> regions) of my proteins prior to the production MD run using some enhanced
> sampling workflow applicable to the selected protein regions.  I  suppose
> that force field based simulated annealing using Langevens dynamics as the
> thermostat and positions restraints applied to the all protein atoms but
> not for loops for which I'd like to find native-like conformations is
> exactly what I look for. Could someone suggest appropriate SA setups for
> such task: e.g number of SA windows, coupling constants in each windows,
> appropriate implicit solvent models?
>
>
>
> TFH,
>
> James
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