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

[Aishwary Shivgan]

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.

Thank you,
Aishwary



On Thu, Dec 8, 2016 at 12:17 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/7/16 11:06 AM, Aishwary Shivgan wrote:
>
>> Hello everyone,
>>
>> Generally the +/- works for bonds, angles, dihedral for the molecules
>> connected linearly but Is there a way to define the +/- connections of a
>> new residue which is connected by 3 different residues.
>>
>>
> pdb2gmx can only create linear connections via .rtp entries, but can
> create branch points via entries in specbond.dat.
>
> -Justin
>
> --
> ==================================================
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
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> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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