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
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Received on Thu Oct 06 2011 - 23:00:03 PDT
