[AMBER] acetyl lysine

From: Dhiraj Srivastava <dhirajks.gmail.com>
Date: Sat, 7 Mar 2015 16:15:29 -0600

Hi all
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?
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

Thank you
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Received on Sat Mar 07 2015 - 14:30:03 PST
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