Hi, Dr.
Thank you for the response.
I've tried to use CT atomtype from the GLYCAM for the acyl chain but when I ran parmchk and generated the frcmod file, there are angles, bonds and dihedral angles that requires attention (ATTN, need revision).
How do you resolve this and where should I refer to get the values?
Thank you, Dr.
Razil.
________________________________
From: Dr. Anselm Horn <anselm.horn.fau.de>
Sent: Monday, July 19, 2021 5:11 PM
To: amber.ambermd.org <amber.ambermd.org>
Subject: Re: [AMBER] Building Forcefield for Glycolipid Molecule
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, Stéphane'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 Tue Jul 20 2021 - 19:00:02 PDT
