[gmx-users] Defining +/- in the RTP file for a molecule with 3 different molecules

[Aishwary Shivgan]

Thanks for the reply.

I will try to implement specbond in my system. Just want to ask if it could
be implemented for the following molecule having multiple branch points in
a single molecule?

http://www.sigmaaldrich.com/content/dam/sigma-aldrich/
life-science/biochemicals/migrationbiochemicals1/
complex-tetraantennary-glyc.jpg

Ultimately I want to attach the glycan to the protein.

Thank you,
Aishwary






On Thu, Dec 8, 2016 at 2:26 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/7/16 11:58 AM, Aishwary Shivgan wrote:
>
>> Hello everyone,
>>
>> Thank you Justin, for the reply.
>>
>> My system is a complex glycan and has many such branch points. Attached
>> the
>> picture of the one I am working on.
>>
>> I am looking at the contents of the specbond.dat
>>
>> Could you help me understand how this works for one of the lines in the
>> specbond.dat
>>
>> CYS     SG      1       HEM     CAB     1       0.18    CYS2    HEME
>>
>>
>> Another option would be to write the rtp for the whole molecule but that
>> would become very big. What I am aiming for is to define different sugars
>> as different residues so that I can build any type of the glycan from
>> available sugars in rtp file.
>>
>>
> Please read manual section 5.7.7.
>
>
> -Justin
>
> --
> ==================================================
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
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> 20 Penn St.
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> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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