Re: [AMBER] Building Forcefield for Glycolipid Molecule

From: Dr. Anselm Horn <anselm.horn.fau.de>
Date: Mon, 19 Jul 2021 11:11:43 +0200

Razil,

some time ago we used a (somehow) similar system, namely trehalose with
two acyl chains. To be consistent within the ligand system (and to avoid
any cross-terms between forcefield borders), we decided to use only
Glycam atom types there and applied the Glycam charge parameterization
scheme.

If you are interested, have a look into the Supplementary material there:
https://doi.org/10.1038/s41598-018-23624-8

But I guess, St├ęphane's work might be more related to your ligand system.

Good luck,

Anselm


On 07/18/2021 07:02 PM, Razil Tahir wrote:
> Hello experts,
> I'm currently trying to build a forcefield for a glycolipid molecule. I'm using the GLYCAM forcefield for the sugar headgroup but there's no parameter for the alkyl chain.
> I've calculated the partial charges using Gaussian09 and took the parameters for the alkyl chain from the GAFF forcefield.
> Is this method practical and correct to be used? Please advise.
>
> Thank you.
>
>
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Received on Mon Jul 19 2021 - 02:30:02 PDT
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