[gmx-users] Rhamnose on 53a6

Justin A. Lemkul jalemkul at vt.edu
Mon Jun 11 12:18:28 CEST 2012

On 6/11/12 6:06 AM, Thales Kronenberger wrote:
> Have you tryed online servers as http://davapc1.bioch.dundee.ac.uk/prodrg/ or
> the Acpype (with Amber)?

For Gromos parameterization, ATB produces much better results than PRODRG.


Validation is always required, though :)


> 2012/6/11 Marc Gordon <marcgrdn55 at gmail.com <mailto:marcgrdn55 at gmail.com>>
>     Hello again fellow gromacs users.
>     I am looking to model a glucose-rhamnose disaccharide using the 53a6
>     forcefield. I wanted to take a look at the naming conventions for
>     carbohydrates but I'm battling to find anything in the pdb2gmx force field
>     files.
>     I downloaded a package of force fields from the GROMOS website to get an
>     idea about naming conventions for carbohydrates and couldn't see any mention
>     of rhamnose anywhere. (allose, altrose, glucose, mannose, gulose, idose,
>     galactose and talose are mentioned but no rhamnose).
>     Does anyone have any information on naming conventions for rhamnose or
>     whether or not rhamnose was ever present in this force field?
>     Regards
>     Marc
>     --
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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