[gmx-users] Protein preparation

[Quin K]

Thank you for the reply.

I have another question. I used MODELLER on Chimera to fix the protein and
found that there were significant visible changes to structure of protein.
I'm not sure whether to use the old protein or the fixed one.
Does it really matter that I used unfixed protein if the structure of
binding site(s) and important chain features remain the same ?
For the 50 ns MD simulation I never fixed the protein.

Regards
Quin.

On Sun, Mar 26, 2017 at 7:51 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/26/17 9:44 AM, Quin K wrote:
>
>> Hi
>>
>> I'm new to Gromacs.
>> I have a question regarding protein preparation for MD simulation.
>>
>> I ran a 50 ns MD simulation but later found out that the protein has a
>> charge.
>> I found that there is a Mg2+ Ion in the protein crystal structure. Should
>> I
>> remove this Mg2+ ion from protein before addition of ions to the protein
>> ??
>>
>> Following is the protein I used.
>>
>> http://www.rcsb.org/pdb/explore.do?structureId=3a5j
>>
>>
> If the ion is catalytically or structurally significant it should be
> retained. If it's a consequence of some crystallization medium and may not
> be relevant in solution or for whatever your purposes are, then it can be
> removed.  But that's your homework to do based on your understanding of the
> biology and the goals of your work.
>
> -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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