Re: AMBER: help with phosphotyrosine

From: Samantha Kaye <>
Date: Tue, 17 Jul 2007 14:00:23 +0100

Thanks David, that worked.

For any other newbies with the same problem, I downloaded both the and frmod_y2p files (I found the amber_typ.lib didn't work,
there seems to be a line missing at the top of the file) to my working
directory. I had to hand edit my PDB file to make sure the residue name
was Y2P and the atom types matched the names given in the OFF file. When
I launched xleap I did the following:

> loadamberparam frmod_y2p
> loadOff

Then I could load my pdb file in the usual way with no complaints.
Hope this helps.


David A. Case wrote:
> On Mon, Jul 16, 2007, Samantha Kaye wrote:
>> I realise this question has been asked before but I can't find a definitive
>> answer, how do I parameterise a phosphotyrosine residue?
> Look at the "contributed parameters" database at the Amber web sight. You
> will download a library file for phosphotyrosine from there, and load that
> into LEaP before loading your pdb file.
> ...good luck...dac
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Jul 18 2007 - 06:07:42 PDT
Custom Search