Re: accelerated MD as the engine for loop refirement

From: James Starlight (
Date: Thu Jul 10 2014 - 04:39:17 CDT

Thanks a lot for suggestions!

So In fact you give me evidence that it's for my task (see a full set of
loop confirmations and chose most probable) will not good to use implicit
solvent +amd because this will produce very unphysical thermodynamics isn't

In fact I'm dealing with the membrane protein where membrane-embeded part
should be fixed (I would not refine something here) and loops which are
exposed to the solvent must be free to move. In this regards I've tried to
applied gb model of IS with the frozen of not refined part of my protein.
Will it be reasonable to use REMD with such implicit solvent model for
refinement? How It could be possible to really simplify REMD protocol for
such loop prediction (e,g using small number of replicas or not).
Some another suggestions besides Brut force md?


2014-07-09 22:22 GMT+02:00 Ajasja Ljubetič <>:

> Perhaps Rosetta <>/pyRosetta
> <> might be worth a look,
> as these even have a dedicated loop refinement protocol.
> Regards,
> Ajasja
> On 9 July 2014 21:39, James Starlight <> wrote:
>> Dear NAMD users!
>> I wounder whether the accelerated molecular dynamics might be good
>> solution for the loop refirement of models made by means of hoology
>> modeling with the teplated which has the low sequence identify in loop
>> region? For instance I've just built some models of membrane receptors
>> agains receptor with known structures and would like to refine loops by
>> some enhansed sampling engine to sample all possible conformation and found
>> most propable during short simulation. Does the acceleraed md good
>> sollution for such task assuming simulation with implicit solvent with
>> restrained all atoms of the helix regions of the refined protein but not
>> loops flexible region? What alternatives should I explored also?
>> TFH,
>> James

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