Dear Gorka,
You may want to take a look at the following paper. It describes the force
field parameters they used to run simulations of structures with acetylated
lysine.
Effects of Posttranslational Modifications on the Structure and Dynamics of
Histone H3 N-Terminal Peptide by: Haiguang Liu, Yong Duan
http://www.cell.com/biophysj/retrieve/pii/S0006349508703254
-ramu
On Oct 7, 2011 7:48 AM, "Ramu Anandakrishnan" <
ramuanandakrishnan55.gmail.com> wrote:
> Dear Gorka,
>
> You may want to take a look at the following paper. It describes the force
> field parameters they used to run simulations of structures with
acetylated
> lysine.
>
> Effects of Posttranslational Modifications on the Structure and Dynamics
of
> Histone H3 N-Terminal Peptide by: Haiguang Liu, Yong Duan
> http://www.cell.com/biophysj/retrieve/pii/S0006349508703254
>
> -ramu
> On Oct 7, 2011 1:55 AM, "FyD" <fyd.q4md-forcefieldtools.org> wrote:
>> Dear Gorka
>>
>>> I would like to use the AMBER forcefield along with an algorithm that
>>> optimizes the protein-dna interface. The problem is that one lysine is
>>> acetylated and I do not have the parameters for this modified residue so
> I
>>> can not run the simulation. I was wondering if any of you had the
> parameters
>>> for the acetylated lysine. If so, I would be grateful if you could send
> them
>>> to me. Looking forward to hearing from you.
>>
>> For acetylated lysine, you only need charge values in a force field
> library.
>> You could use R.E.D. Server to generate a new FF library for this
>> modified amino-acid.
>>
>> You need to prepare a P2N file & you generate automatically the FF
>> libraries for the N-term, C-term & central fragments and the dipeptide
>> from this dipeptide in a single step.
>>
>> (You also need to decide which conformation to use for the side chain
>> & backbone)
>>
>> See
>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
>> versus
>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
>>
>> regards, Francois
>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Fri Oct 07 2011 - 05:00:02 PDT
