Re: [AMBER] GLYCAM naming

From: Lachele Foley <>
Date: Thu, 7 Jul 2016 15:45:13 -0400

For the modular nature of the glycam parameters to work, you will need
seven residues. That is, you need to explicitly specify the nature of the
moiety attached to the anomeric carbon at the reducing end. If you intend
that to be a hydroxyl group (and not O-Me or O-tBt), call it ROH. If you
are using a PDB file that contains the reducing-end oxygen, that oxygen
needs to be split out to a separate residue called ROH. You will need to
alter the residue numbers, but the serial numbers for the atoms don't have
to change.

On Thu, Jul 7, 2016 at 2:56 PM, Fabrício Bracht <> wrote:

> I am building the model with a molecule consisting of 6 glucoses Beta
> linked. I have the structures without any hydrogens, and am trusting tleap
> to add hydrogens for me. The naming for the second to the fifth would 4GB,
> the sixth I've named 0GB. From what I guessed, the first residue, which has
> a bond on carbon 4 but the hydroxyl on carbon 1 free, should be called 4GB
> also, but that does not seem to work. Tleap places all hydrogens correctly
> on residues 2 to 6, but glucose 1 remains with the hydroxyl on carbon 1
> without its hydrogen.
> What am I doing wrong here?
> Thank you
> Fabrício
> _______________________________________________
> AMBER mailing list

:-) Lachele
Lachele Foley
Athens, GA USA
AMBER mailing list
Received on Thu Jul 07 2016 - 13:00:02 PDT
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