Razil,
the choice of atom types in a unit to be parameterized is crucial for
its forcefield description, since from the combination of bonded atoms,
triples (angle terms), and quadruples (torsion terms) it is determined,
whether force field parameters already exist or not.
We did not use atom type CT for our approach for acyl chain atoms;
like Stephané, we used a RESP charge generation approach (via the
RED-Server), similar to the orginal Glycam philosophy. This is all
described in detail in the Supplementary Material of our manuscript.
If parameters are missing or marked as need revision, parameters from
similar terms may potentially be used. Then, however, test simulations
should be run to ensure the validity of this approach.
Good luck
Anselm
On 07/21/2021 03:36 AM, Razil Tahir wrote:
> 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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>>
>
>
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Received on Wed Jul 21 2021 - 02:00:02 PDT
