Re: [AMBER] Molecule with glyco - single amino acid linkage?

From: Lachele Foley <>
Date: Mon, 8 May 2017 00:32:46 -0400

Use the ZOLS residue (ZOLS stands for zwitterion O-linked serine). We
don't have every relevant amino acid, but we have that one.

You should be able to use something like the following. Here, I assume you
want to attach a beta-D-glucopyranos to a zwitterionic serine:

source leaprc.protein.ff14SB
source leaprc.GLYCAM_06j-1
m = sequence { ZOLS 0GB }

Then, just save whatever files you normally would. Let me know if that
doesn't work.

On Sun, May 7, 2017 at 11:25 PM, yunshi11 . <> wrote:

> Dear all,
> I understand that you can easily build glycoprotein or glycopeptide in LEaP
> of AMBERTOOLS, using Glycam_06 and Amber ff12SB/ff14SB force fields. But
> how about sugars linked to a single amino acid in a way analogous to
> glycosylation?
> For a single Serine (linked via O-glycosylation to a sugar residue) , I'd
> like to have both N-terminal and C-terminal present (i.e. -NH3+ and -COO-),
> but the official Glycam libraries (GLYCAM_amino_06j_12SB,
> GLYCAM_aminoct_06j_12SB, GLYCAM_aminont_06j_12SB) only contain those for
> either N-term or C-term residues, not both.
> So is there a library for glycosylation on single amino acids? Has anyone
> seen publications on parameters for such molecules?
> Best regards,
> Yun
> _______________________________________________
> AMBER mailing list

:-) Lachele
Lachele Foley
Athens, GA USA
AMBER mailing list
Received on Sun May 07 2017 - 22:00:03 PDT
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