Hi Guowei,
I am not aware of any existing AMBER topologies and partial atomic
charges for methylated lysine. You will probably need to create this
residue yourself. There are AMBER tutorials that will help guide you
through the process, including calculating AM1-BCC charges that should be
fairly compatible with the protein force field (e.g. Parm14SB). I assume
that the methylated lysine is part of a protein sequence, which means you
will most likely need to stick to the protein force field (as apposed to
using GAFF). You may also come across missing parameters associated with
lysine's NZ atom type - I am thinking about the associated C-N-C bending
and C-C-N-C torsion terms.
Bests,
Karl
On Tue, Jan 12, 2016 at 8:13 PM, Yin, Guowei <guowei_yin.med.unc.edu> wrote:
> Hi all,
>
> I want to run simulation for protein containing Lysine with
> Mono-methylation. Where can I find the force field parameters including top
> and charges etc.?
>
> Thank you,
> Guowei
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Received on Wed Jan 13 2016 - 02:30:04 PST
