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.
http://compbio.biosci.uq.edu.au/atb/
Validation is always required, though :)
-Justin
2012/6/11 Marc Gordon <[email protected] <mailto:[email protected]>>
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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