[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
> 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?
> gmx-users mailing list gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users