Re: [AMBER] Force field for terminal phosphorylated residues

From: David A Case <>
Date: Tue, 18 Feb 2020 08:35:16 -0500

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.


AMBER mailing list
Received on Tue Feb 18 2020 - 06:00:03 PST
Custom Search