Thank you! I am trying to simulate the Schiff base for my protein in which
lysine is binding the fructose molecule through a covalent bond NZ-C1 of
fructose. Can I use xleap to build this structure and how. What I have in
my hand that I should separate lysine residue from the protein and attach
it to fructose and then re-ligate, is it correct. I do not know how can
xleap can do.
Regards,
Ibrahim
On Wed, Jan 23, 2013 at 3:21 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Tue, Jan 22, 2013, Ibrahim Said wrote:
>
> > I am a very newbie for Amber. I am trying to construct a protein and
> > fructose complex but I can not find a procedure or a tutorial steps to
> > carry out.
>
> You don't say whether this is a covalent or non-covalent interaction
> between
> the protein and the fructose. For a covalent interaction, the glycam
> builder
> may help; non-covalent interactions would handle fructose like any other
> ligand: use load both the protein ff you want and the glycam ff.
>
> ...dac
>
>
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Received on Wed Jan 23 2013 - 09:30:02 PST
