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

[Felix Y Yang]

Thanks for the reply.

I'm trying to test out a theory that enzymes gain "heat" from their
substrate after the catalytic reaction finishes, thus my plan to heat up
the active site. Is there a better approach to testing this theory?

How would I specify the groups?

Felix


>
>
> 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
>
> --
> ==================================================
>
> 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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