Hi Francois,
I am trying to understand how this works.
So instead of combining individual residues in a building-block manner, as
in the assignment of atomic charges for proteins with amber99sb, it is
recommended to consider the ligand as a holistic molecule when calculating
the RESP charge? I am curious that if I could do things in a building-block
manner since it can potentially decrease a lot of computational time for
geometry optimization.
And when it comes to geometrical parameters, we should use GLYCAM for sugar
part, 99SB for standard amino acids, and GAFF for organic part?
BTW, could you tell me how to generate multiple conformations with geometry
optimization from Gaussian 09?
Thanks,
Yun Shi
On Sat, Aug 20, 2011 at 12:07 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Yun,
>
> > Is it technically possible to do it due diligence in the first place?
> That
> > is, cut the molecule into three parts as I mentioned before, use GLYCAM
> for
> > the sugar part, 99SB for the Thr, and GAFF for modified Phe and the
> > thio-glycosidic linkage. And may I then link these parts together using
> LEaP
> > ?
>
> Concerning the use of GLYCAM + GAFF + Amber99SB you might be
> interested by looking at the following paper:
> http://www.ncbi.nlm.nih.gov/pubmed/21792425
> & its corresponding R.E.DD.B. project .
> http://q4md-forcefieldtools.org/REDDB/projects/F-85/ + its LEaP script:
> http://q4md-forcefieldtools.org/REDDB/projects/F-85/script1.ff
>
> This work is about cyclodextrin based-glycopeptide and 1-4 non-bonding
> interactions in GLYCAM & Amber99SB.
>
> Your structure is not a cyclodextrin but this work describe (i) how to
> derive charges and build force field libraries for new fragments by
> using R.E.D. IV and (ii) proposes new directions concerning the
> treatment of 1-4 non-bonding interactions in the context of
> glycopeptides.
>
> Finally, in the LEaP script you will find examples how to connect
> organic, amino-acid and monosaccharide units...
>
> regards, Francois
>
>
>
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Received on Wed Aug 24 2011 - 16:30:03 PDT
