Re: [AMBER] acetyl lysine

From: David A Case <>
Date: Sat, 7 Mar 2015 20:43:48 -0500

On Sat, Mar 07, 2015, Dhiraj Srivastava wrote:

> I am trying to simulate my protein which is acetylated. I am using ALY as 3
> letter code for acetyl lysine. however xleap is saying unknown residue
> type. i tried f14SB and ff99SB. what is the name of acetyl lysine residue
> in AMBER? which amber forcefield should i use for acetyl lysine?

None of the standard Amber libraries have this modification. I'd suggest
first looking at the Amber_PTM (post-translational modifications) library --
there is a link on the Amber web site.

> Also, I am trying to simulate a mutant of my protein whose structure is not
> known. however converting the serine to glutamate is causing steric clash
> and my simulation become unstable. what is the best way to solve this
> problem?

How much initial minization did you carry out? What exactly do you mean
by saying that your simulation "became unstable"? How did you perform the
mutation in the first place? You don't need to answer these questions
here: they are more questions to ask yourself. Be sure to visualize the
glutamate simulation: what is the bad clash? Could you get rid of it by
starting with a different side-chain rotatmer?


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Received on Sat Mar 07 2015 - 18:00:03 PST
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