[gmx-users] Protein preparation

[Rasika Kelum]

Thank you Justin. Highly appreciate your help.

If there are missing residues, any suggestions on fixing the protein?

1. How to find correct sequence? (is there any website to find correct
sequence?)
2. How to FIX the sequence (using what software?)
3. Once residues are fixed how would that affect the geometry of the
protein? Do we have to fix the geometry of protein as well?

Thanks!!

Regards
Quin

On Mar 27, 2017 1:47 AM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> On 3/26/17 12:39 PM, Quin K wrote:
>
>> 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.
>>
>>
> This all depends on what "fixed" means.  Were there missing residues?
> Clashes in the structure?  In the case of the former, without a "fix" then
> the missing residues will cause lots of problems.  In the case of the
> latter, energy minimization is usually sufficient to alleviate any problems.
>
> -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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