Re: AMBER: phosphorylated residues

From: David A. Case <>
Date: Mon, 2 Apr 2007 15:13:37 -0700

On Mon, Apr 02, 2007, yxamber wrote:

> There are two phosphorylated residues in my protein,
> TPO183 (phosphorylated threonine) and PTR185 (phosphorylated tyrosine).I
> have modified the two residues in the pdb file as follows: the residue name
> of the atoms belong to the THR183 and TYR185 were modified back to THR and
> TYR respectively; the residue name of the two phosphate groups were deleted
> and the residue number of them were modified to 359 and 360 (the last
> residue number in my protein was 358, so I add two residue number for
> them).Though the parameters of the phosphate group atoms were included in
> the amber9/dat/leap/parm/parm99.dat, the 8 phosphate group atoms were not
> recognized by leap.

What you should do is go to the contributed parameters database (look for this
on the Amber web page), and get the units for phosphorylated amino acids you
need. Modify your pdf file so that the residue and atom names in the pdb file
match those in the downloaded libraries.

...good luck...dac

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Received on Wed Apr 04 2007 - 06:07:31 PDT
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