[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.
https://ambermd.org/tutorials/basic/tutorial5/index.php
How would this option compare?


Thank you!

Best wishes,
Mingxuan Jiang

Postgraduate
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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