Looking at those parameters I wonder though why some of the carbon
charges are so different from the standard force field and among
themselves esp. CB.
URLs are case sensitive btw.
On Wed, 13 Jan 2016 15:52:45 +0530
<amin.imtech.res.in> wrote:
>
>
> 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
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>
>
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Received on Wed Jan 13 2016 - 03:30:03 PST
