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 Sat Aug 20 2011 - 00:30:03 PDT
