Re: [AMBER] parameters for Mono-methylated Lysine

From: <>
Date: Wed, 13 Jan 2016 15:52:45 +0530


Hi. The parameters for methylated lysine are available from Dr. DIMITRIS


Hope they can be used or be good starting points.



On 2016-01-13 15:50, Karl Kirschner wrote:

> 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 <> 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 _______________________________________________ AMBER mailing list [1]
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Received on Wed Jan 13 2016 - 03:00:04 PST
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