[AMBER] Enquiry about the Best way to Simulate Phosphorylated Tyrosines

From: Mingxuan Jiang via AMBER <amber.ambermd.org>
Date: Fri, 10 Nov 2023 19:31:46 +0000

Dear Sir/Mdm,

I have an enquiry on what is the best approach to simulating phosphorylated residues.

I have come across 3 different methods, each with their pros and cons, and I am not quite sure how to proceed.

Approach 1)
In previous forum posts many years ago, parameters from http://amber.manchester.ac.uk/ were recommended, but I am not sure if they are still up to date with the latest parameterisations or if they are compatible with forcefields like ff14SB or ff19SB

Approach 2)
CHARM-GUI is able to parameterise the residues provided. However, it seems to always protonate the PO4 2- phosphate group to become PO4H instead, which is not desirable for the simulation. I have asked CHARM-GUI forums for a way to solve this problem

Approach 3)
I have parameterised custom-residues using this excellent tutorial here before, with antechamber, RESP and prepgen.
How would this option compare?

Thank you!

Best wishes,
Mingxuan Jiang

Creixell Lab
CRUK Cambridge Institute
University of Cambridge

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Received on Fri Nov 10 2023 - 12:00:03 PST
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