Mingxuan,
parameters for the most common phosphorylated amino acids are available
within Amber; it is also described in the manual.
Our original parameter set (still available on the website of
contributed parameters, Bryce group) was updated by the Amber developers
and included into the Amber distribution, then adapted to newer force
fields, so that now parameter sets also for parm14SB and parm19SB exist.
(Just for your reference: the atomic charge set has not changed and is
still from the original work; this is thus a demonstrated case for
continous and consistent parameter development, IMHO.)
Best,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
On 11/10/2023 08:31 PM, Mingxuan Jiang via AMBER wrote:
> 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
>
> [signature_3923700459] [signature_3619670221]
>
>
>
>
>
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Received on Sat Nov 11 2023 - 00:30:03 PST
