[gmx-users] From: Graduate Student protein active site inquiry

[Justin Lemkul]

On 5/5/17 6:56 PM, Felix Y Yang wrote:
> Good afternoon,
>
> I am a graduate student working at UCSD, and currently working on a few
> simple proteins like beta-amylase, insulin, and triosephosphate isomerase
> in gromacs. I'm fairly new to protein simulations in general, and I would
> like to know if there is a way to identify and isolate the active sites on
> these proteins in an index file to heat individually from the rest of the
> protein as part of a simulation I plan to do. Any feedback would be
> greatly appreciated, thank you.
>

You can specify groups as tc-grps and then corresponding groups for simulated 
annealing.  What you're proposing is extremely unphysical, though.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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