Re: [AMBER] Nonstandard residue: phosphotyrosine

From: Jason Swails <>
Date: Mon, 29 Oct 2012 11:05:43 -0400

The problem here is that your phosphotyrosine connects to residues on
either side of it. As a result, there are bonds between atoms in your
phosphotyrosine (whose atom types are gaff atom types) and atoms in the
rest of your protein (whose atom types are Amber atom types). Since these
bonds (and corresponding angles and dihedrals) do not appear in your TRS
residue, parmchk does not know to look for them (nor could it find them).

This is why you are getting these errors. For phosphotyrosine, your
residue really should be typed like the AMBER force fields, not like the
gaff force field. You can do this via the "-at amber" flag in antechamber
(run antechamber with no arguments to get the full usage).

However, you should carefully check that the atom types in your residue
matches the atom types in the normal tyrosine residue where appropriate.

However, AmberTools 12 includes a library file with phospho-amino acids
(among them phosphotyrosine (-2), phosphoserine (-2), phosphothreonine
(-2), phosphohistidine (-2), phosphotyrosine (-1), phosphoserine (-1), and
phosphothreonine (-1). See $AMBERHOME/dat/leap/lib/phosphoaa10.lib and the
corresponding phosphoaa10.readme file that has the information as well as
the published reference with the parametrization.

Unless you are interested in going through the exercise as an example, I
would suggest using these parameters instead.

Good luck,

On Mon, Oct 29, 2012 at 10:46 AM, PAUL NEWMAN <> wrote:

> Hello Anselm,
> Thanks for fast reply. I am not an expert building force fields, and yes I
> am doing it just because I need it. Could you please be more especific?
> I compared the lib files and it looks that they are consistent. However
> there is no FRCMOD files availables to compare.
> Please any expert building force field that can point out what is wrong; I
> will highly appreciate it.
> Thanks
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Mon Oct 29 2012 - 08:30:03 PDT
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