You just need to change the linking residue in the protein to NLN
(N-linked asparagine). That residue has the appropriate charge
modification that the resulting charge will be integral. If you have
loaded one of the recent GLYCAM leaprc's, NLN should already be
available. Just remember to remove from the PDB file the hydrogen, if
it is present, that the glycan will be replacing.
On Thu, Jul 24, 2014 at 12:28 PM, Tommaso Casalini
<tommaso.casalini.mail.polimi.it> wrote:
> Dear Amber users and developers,
> I would like to simulate a glycoprotein, whose structure is available in
> pdb database.
> In particular, there is this branched chain:
>
> 4YB - 4YB - VMB - OMA - OMA
>
> This chain is attached to the protein through a ND2 - C1 bond with an ASN
> residue.
> The net charge of the chain is not equal to an integer value, but equal to
> 0.194; this is consistent with the charge of the ending group -ROH (-0.194)
> that should be added for an isolated chain.
>
> My question is: which is the best strategy to obtain an integer value of
> the overall charge?
>
> Thank you for your help.
> Kind regards,
> Tommaso Casalini
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Thu Jul 24 2014 - 10:30:02 PDT
