Dear Dhiraj,
there is an article about chromatin interactions with differently modified
histone tails by George V. Papamokos et al. in which they use parameters
for acetylated and methylated lysine. (DOI: 10.1016/j.bpj.2012.03.030)
The parameters can be downloaded at
http://pc164.materials.uoi.gr/dpapageo/amberparams.php.
with kind regards,
Achim Sandmann
> 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?
>
> ....dac
>
>
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Received on Mon Mar 09 2015 - 02:30:02 PDT
