Re: [AMBER] Force field for terminal phosphorylated residues

From: Ming Tang <>
Date: Wed, 19 Feb 2020 05:37:23 +0000

Hi David,

Thanks for your suggestion.

I found my pThr2 locates in the N-terminus. Will it also be protonated into T1P with a net charge of -1?


-----Original Message-----
From: David A Case <>
Sent: Tuesday, 18 February 2020 11:35 PM
To: AMBER Mailing List <>
Subject: Re: [AMBER] Force field for terminal phosphorylated residues

On Tue, Feb 18, 2020, Ming Tang wrote:
>I found that amber does not treat phosphorylated residues (e.g., pThr)
>differently when they locate in the protein terminal. This results in
>the situation that terminal phosphothreonine (TPO) has a charge of
>negative 3. Is this reliable?

I don't know of any Amber library entries for C-terminal phosphorylated amino acids, so I don't know how you built your protein. The TPO residue in leaprc.phosaa10 is for a pThr in the middle of a chain.

I don't know of any litereature on the pKa of a pThr when it is at the C-terminus, but there may be some. My guess is that the side chain would be more likely to be protonated (i.e. in the -1 charge state), due to the influence of the COO- group.


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