[gmx-users] Loop refirement using simulated annealing

Christopher Neale chris.neale at alum.utoronto.ca
Tue May 27 22:22:08 CEST 2014

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.


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?


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