Hi. The parameters for methylated lysine are available from Dr. DIMITRIS
PAPAGEORGIOU'S WEBSITE
HTTP://PC164.MATERIALS.UOI.GR/DPAPAGEO/AMBERPARAMS.PHP
Hope they can be used or be good starting points.
Regards,
Amin.
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 <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 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber [1]
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber [1]
Links:
------
[1]
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jan 13 2016 - 03:00:04 PST
