Question about parametrizing glycolipids in SIRAH

[lizsuarez002]

Hello SIRAH team,

I am currently trying to test the inhibition of some ligands, specifically glycolipids, against a protein using the SIRAH force field. However, I am facing difficulties with the parametrization of these ligands, since they are not present in any of the available databases.

My main question is whether SIRAH provides a specific force field or mapping strategy for glycolipids. If not, should these ligands be treated separately, for example by parametrizing the glycosidic headgroup on one side and the lipid tail on the other?

In other words, I would like to know if it is even possible to model glycolipids within the current SIRAH framework.

Any guidance, recommendations, or references would be very helpful.

Thank you very much in advance for your support.

Best regards,

[SIRAHFF]

Hi! Unfortunately, parameterization might not be straightforward. In principle, if the glycans are already available, binding them to existing lipids could be an option Also, because of some technical issues with 1-4 interactions at branching points. Most glycans are limited to the AMBER engine. Which lipid are you interested in? Eventually, we can help you in parametrizing your molecule. Best, Sergio El jue, 28 ago 2025 a las 12:37, lizsuarez002 ***@***.***>) escribió:

…

Hello SIRAH team, I am currently trying to test the inhibition of some ligands, specifically glycolipids, against a protein using the SIRAH force field. However, I am facing difficulties with the parametrization of these ligands, since they are not present in any of the available databases. My main question is whether SIRAH provides a specific force field or mapping strategy for glycolipids. If not, should these ligands be treated separately, for example by parametrizing the glycosidic headgroup on one side and the lipid tail on the other? In other words, I would like to know if it is even possible to model glycolipids within the current SIRAH framework. Any guidance, recommendations, or references would be very helpful. Thank you very much in advance for your support. Best regards, — Reply to this email directly, view it on GitHub <#99>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BB2GKHHUSW2YKGUIGYUWCBL3P4O3HAVCNFSM6AAAAACFB26S52VHI2DSMVQWIX3LMV43ERDJONRXK43TNFXW4OZYHAYTCNRYGA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>