Re: [AMBER] Phosphotyrosine connectivity problem

From: David A Case <>
Date: Mon, 19 Dec 2011 08:14:24 -0500

On Mon, Dec 19, 2011, Sangeetha B wrote:
> I am simulating a protein which contains two phosphotyrosine residues using
> Amber 11 and ff99SB force field.
> For the parameters of Phosphotyrosine with single protonated phosphate
> group, i used the ones available at
> The structure obtained after 1000 cycles of minimization showed some
> connectivity problem in the phosphate group. An image showing the lack of
> connectivity between one of the phosphate oxygens is attached with this
> mail.

You don't say how the image was made, but most molecule viewing programs draw
bonds based on assumptions about distances between atoms. You might want to
compare the four O-P bond lengths in the minimized structure.

If you use VMD, and load the prmtop file first, then VMD will use the
bonds in the prmtop file to decide which bonds to draw on screen. Other
programs may have similar options. You can also use rdparm to print a
list of the bonds in your system; in any event, these don't change upon

I agree that it is odd that the atom names (not atom types, which are not
present a pdb file) are OP1, OP2 and O3P. But you can probably track that
down somehow.


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Received on Mon Dec 19 2011 - 05:30:06 PST
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