On Fri, Oct 28, 2016, Nikolay N. Kuzmich wrote:
>
> I'm going to conduct MD simulation for protein molecule
> which has some covalently bound oligosaccharide residues.
> Should I treat these residues separately by the specially designed
> forcefield
> (e.g. GLYCAM) ?
Yes. The glycam web site (glycam.org) has lots of tools to help with this.
For example, if you have an xray structure from the PDB, it can help convert
that to Amber format. Or, if you want to build a starting structure for a
given sugar onto a protein, the web site can help with that as well.
....dac
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Received on Fri Oct 28 2016 - 07:00:02 PDT
